Package 'RDML'

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.
Authors: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut] , Andrej-Nikolai Spiess [aut]
Maintainer: Konstantin A. Blagodatskikh <[email protected]>
License: MIT + file LICENSE
Version: 1.3
Built: 2024-12-28 04:40:47 UTC
Source: https://github.com/pcruniversum/rdml

Help Index

Extract data points from RDML object

Description

Extract data points from RDML object as.data.frame.

Usage

## S3 method for class 'RDML'
x[i, j, dp.type = "adp"]

Arguments

x

RDML object.
i, j

indices.
dp.type

Type of fluorescence data (i.e. 'adp' for qPCR or 'mdp' for melting).

adpsType R6 class.

Description

adpsType R6 class.

adpsType R6 class.

Format

An R6Class generator object.

Details

Contains matrix of amplification data. Must have three columns:

cyc

PCR cycle at which data point was collected (every cycle must have unique number).

tmp

temperature in degrees Celsius at the time of measurement (optional).

fluor

raw fluorescence intensity measured.

Inherits: rdmlBaseType.

Initialization

adpsType$new(fpoints)

Fields

fpoints

assertMatrix. Matrix with amplification data points.

Super class

RDML::rdmlBaseType -> adpsType

Methods

Public methods

Inherited methods

Method new()

Usage
adpsType$new(fpoints)

Method .asXMLnodes()

Usage
adpsType$.asXMLnodes(node.name)

Method clone()

The objects of this class are cloneable with this method.

Usage
adpsType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

#cycles
cyc <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40)
#fluorescence
fluo <- c(2.0172, 2.0131, 2.0035, 2, 2.0024, 2.0056, 2.0105, 2.0179,
2.0272, 2.0488, 2.0922, 2.1925, 2.3937, 2.7499, 3.3072, 4.0966,
5.0637, 6.0621, 7.0239, 7.8457, 8.5449, 9.1282, 9.6022, 9.9995,
10.2657, 10.4989, 10.6813, 10.8209, 10.9158, 10.9668, 11.0053,
11.0318, 11.0446, 11.044, 11.0052, 10.9671, 10.9365, 10.9199,
10.897, 10.8316)
#temperature
temp <- c(55, 55, 55, 55, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55,
55, 55, 55, 55, 55, 55, 55, 55, 56, 55, 55, 55, 55, 55, 55, 55,
55, 55, 55, 55, 55, 55, 55, 55, 55)

#combine all variables into a proper object
data <- data.frame(cyc = cyc, tmp = temp, fluor = fluo)

#create adps object
adpsType$new(data)

#create adps object without temperature data
adpsType$new(data[, -2])

annotationType R6 class.

Description

Annotate samples by setting a property and its value. For example, sex could be a property with the possible values M or F. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Fields

property

checkString. Property name

value

checkString. Value

Super class

RDML::rdmlBaseType -> annotationType

Methods

Public methods

Inherited methods

Method new()

Usage
annotationType$new(property, value)

Method clone()

The objects of this class are cloneable with this method.

Usage
annotationType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

#set sex property
annotationType$new(property = "sex", value = "M")

Convert idType object to character

Description

Function to convert idType object to character.

Usage

## S3 method for class 'idType'
as.character(x, ...)

Arguments

x

idType object.
...

Further arguments to be passed.

Convert reactIdType object to character

Description

Function to convert reactIdType object to character.

Usage

## S3 method for class 'reactIdType'
as.character(x, ...)

Arguments

x

reactIdType object.
...

Further arguments to be passed.

RDML$AsDendrogram() wrapper

Description

Read more at RDML.AsDendrogram

Usage

AsDendrogram(obj, ...)

Arguments

obj

RDML object.
...

AsDendrogram params.

RDML$AsTable() wrapper

Description

Read more at RDML.AsTable

Usage

AsTable(obj, ...)

Arguments

obj

RDML object.
...

AsTable params.

baseTemperatureType R6 class.

Description

Parent class for inner usage. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

baseTemperatureType$new(duration,
  temperatureChange = NULL, durationChange = NULL, measure = NULL, ramp =
  NULL)

Fields

duration

checkCount. Duration of this step in seconds.

temperatureChange

checkNumber. Change of the temperature between two consecutive cycles: actual temperature = temperature + (temperatureChange * cycle counter)

durationChange

checkCount. Change of the duration between two consecutive cycles: actual duration = duration + (durationChange * cycle counter)

measure

measureType. Indicates to make a measurement and store it as meltcurve or real-time data.

ramp

checkNumber. Allowed temperature change between two consecutive cycles in degrees Celsius per second. If unstated, the maximal change rate is assumed.

Super class

RDML::rdmlBaseType -> baseTemperatureType

Methods

Public methods

Inherited methods

Method new()

Usage
baseTemperatureType$new(
  duration,
  temperatureChange = NULL,
  durationChange = NULL,
  measure = NULL,
  ramp = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
baseTemperatureType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

cdnaSynthesisMethodType R6 class.

Description

Description of the cDNA synthesis method. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

cdnaSynthesisMethodType$new(enzyme = NULL,
  primingMethod = NULL, dnaseTreatment = NULL, thermalCyclingConditions =
  NULL)

@section Fields:

enzyme

checkString. Name of the enzyme used for reverse transcription.

primingMethod

primingMethodType.

dnaseTreatment

checkFlag if TRUERNA was DNAse treated prior cDNA synthesis.

thermalCyclingConditions

idReferencesType.

Super class

RDML::rdmlBaseType -> cdnaSynthesisMethodType

Methods

Public methods

Inherited methods

Method new()

Usage
cdnaSynthesisMethodType$new(
  enzyme = NULL,
  primingMethod = NULL,
  dnaseTreatment = NULL,
  thermalCyclingConditions = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
cdnaSynthesisMethodType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

commercialAssayType R6 class.

Description

For some commercial assays, the primer sequences may be unknown. This element allows to describe commercial assays. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

commercialAssayType$new(company, orderNumber)

@section Fields:

company

checkString.

orderNumber

checkString.

Super class

RDML::rdmlBaseType -> commercialAssayType

Methods

Public methods

Inherited methods

Method new()

Usage
commercialAssayType$new(company, orderNumber)

Method clone()

The objects of this class are cloneable with this method.

Usage
commercialAssayType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

cqDetectionMethodType R6 class.

Description

The method used to determine the Cq value. Can take values:

"automated threshold and baseline settings"
"manual threshold and baseline settings"
"second derivative maximum"
"other"

Inherits: enumType.

Format

An R6Class generator object.

Initialization

cqDetectionMethodType$new(value)

@section Fields:

value

checkString.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> cqDetectionMethodType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
cqDetectionMethodType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

dataCollectionSoftwareType R6 class.

Description

Software name and version used to collect and analyze the data. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

dataCollectionSoftwareType$new(name, version)

@section Fields:

name

checkString.

version

checkString.

Super class

RDML::rdmlBaseType -> dataCollectionSoftwareType

Methods

Public methods

Inherited methods

Method new()

Usage
dataCollectionSoftwareType$new(name, version)

Method clone()

The objects of this class are cloneable with this method.

Usage
dataCollectionSoftwareType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

dataCollectionSoftwareType$new(name = "ExampleSoft",
                               version = "1.0")

dataType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

dataType$new(tar, cq = NULL, excl = NULL,
adp = NULL, mdp = NULL, endPt = NULL, bgFluor = NULL, bgFluorSlp = NULL,
quantFluor = NULL)

Fields

tar

idReferencesType. TargetID - A reference to a target.

cq

checkNumber. Calculated fractional PCR cycle used for downstream quantification. Negative values express following condition: Not Available: -1.0 . (can be NaN for BioRad Maestro compatibility)

excl

checkString. Excluded. If excl is present, this entry should not be evaluated. Do not set this element to FALSE if the entry is valid. Instead, leave the entire excl element out instead. It may contain a string with a reason for the exclusion. Several reasons for exclusion should be seperated by semicolons ";".

adp

adpsType.

mdp

mdpsType.

endPt

checkNumber

. Value of the endpoint measurement.

bgFluor

checkNumber. Background fluorescence (the y-intercept of the baseline trend based on the estimated background fluorescence).

bgFluorSlp

checkNumber. Background fluorescence slope - The slope of the baseline trend based on the estimated background fluorescence. The element should be absent to indicate a slope of 0.0; If this element is present without the bgFluor element it should be ignored.

quantFluor

checkNumber. Quantification flourescence - The fluorescence value corresponding to the treshold line.

Methods

AsDataFrame(dp.type = "adp")

Represents amplification (

dp.type = "adp"

) or melting (dp.type = "mdp") data points as data.frame

Super class

RDML::rdmlBaseType -> dataType

Methods

Public methods

Inherited methods

Method new()

Usage
dataType$new(
  tar,
  cq = NULL,
  excl = NULL,
  adp = NULL,
  mdp = NULL,
  endPt = NULL,
  bgFluor = NULL,
  bgFluorSlp = NULL,
  quantFluor = NULL
)

Method GetFData()

Usage
dataType$GetFData(dp.type = "adp")

Method clone()

The objects of this class are cloneable with this method.

Usage
dataType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

documentationType R6 class.

Description

These elements should be used if the same description applies to many samples, targets or experiments. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

documentationType$new(id, text = NULL)

@section Fields:

id

idType. Identificator.

text

checkString. Text.

Super class

RDML::rdmlBaseType -> documentationType

Methods

Public methods

Inherited methods

Method new()

Usage
documentationType$new(id, text = NULL)

Method clone()

The objects of this class are cloneable with this method.

Usage
documentationType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

dyeType R6 class.

Description

Detailed information about the dye. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

dyeType$new(id, description = NULL)

@section Fields:

id

idType. Identificator.

description

checkString. Description.

Super class

RDML::rdmlBaseType -> dyeType

Methods

Public methods

Inherited methods

Method new()

Usage
dyeType$new(id, description = NULL)

Method clone()

The objects of this class are cloneable with this method.

Usage
dyeType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

enumType R6 class.

Description

Generic class for creating objects thet can take limited list of values.
Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

enumType$new(value)

@section Fields:

value

checkString. Value.

Super class

RDML::rdmlBaseType -> enumType

Methods

Public methods

Inherited methods

Method new()

Usage
enumType$new(value)

Method print()

Usage
enumType$print(...)

Method .asXMLnodes()

Usage
enumType$.asXMLnodes(node.name)

Method clone()

The objects of this class are cloneable with this method.

Usage
enumType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

experimenterType R6 class.

Description

Contact details of the experimenter. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

experimenterType$new(id, firstName, lastName,
  email = NULL, labName = NULL, labAddress = NULL)

@section Fields:

id

idType. Identificator.

firstName

checkString. First name.

lastName

checkString. Last name.

email

checkString. Email.

labName

checkString. Lab name.

labAddress

checkString. Lab address.

Super class

RDML::rdmlBaseType -> experimenterType

Methods

Public methods

Inherited methods

Method new()

Usage
experimenterType$new(
  id,
  firstName,
  lastName,
  email = NULL,
  labName = NULL,
  labAddress = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
experimenterType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

experimentType R6 class.

Description

A qPCR experiment. It may contain several runs (runType). Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

experimentType$new(id, description = NULL,
  documentation = NULL, run = NULL)

@section Fields:

id

idType.

description

checkString.

documentation

list of idReferencesType.

run

list of runType.

Methods

AsDataFrame(dp.type = "adp", long.table = FALSE)

Represents amplification (dp.type = "adp") or melting (dp.type = "mdp") data points as data.frame. long.table = TRUE means that fluorescence data for all runs and reacts will be at one collumn.

Super class

RDML::rdmlBaseType -> experimentType

Methods

Public methods

Inherited methods

Method new()

Usage
experimentType$new(id, description = NULL, documentation = NULL, run = NULL)

Method GetFData()

Usage
experimentType$GetFData(dp.type = "adp", long.table = FALSE)

Method clone()

The objects of this class are cloneable with this method.

Usage
experimentType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

RDML$GetFData() wrapper

Description

Read more at RDML.GetFData

Usage

GetFData(obj, ...)

Arguments

obj

RDML object.
...

GetFData params.

gradientType R6 class.

Description

Details of the temperature gradient across the PCR block. Inherits: baseTemperatureType.

Format

An R6Class generator object.

Initialization

gradientType$new(highTemperature,
  lowTemperature, ...)

Fields

highTemperature

checkNumber. The highest temperature of the gradient in degrees Celsius.

lowTemperature

checkNumber. The lowest temperature of the gradient in degrees Celsius.

...

Params of parent class baseTemperatureType.

Super classes

RDML::rdmlBaseType -> RDML::baseTemperatureType -> gradientType

Methods

Public methods

Inherited methods

Method new()

Usage
gradientType$new(highTemperature, lowTemperature, ...)

Method clone()

The objects of this class are cloneable with this method.

Usage
gradientType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

idReferencesType R6 class.

Description

Contains id of another RDML object. Inherits: idType.

Format

An R6Class generator object.

Initialization

idReferencesType$new(id)

Fields

id

checkString. Identificator.

Super classes

RDML::rdmlBaseType -> RDML::idType -> idReferencesType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
idReferencesType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

idType R6 class.

Description

Contains identificator for varius RDML types. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

idType$new(id)

@section Fields:

id

checkString. Identificator.

Super class

RDML::rdmlBaseType -> idType

Methods

Public methods

Inherited methods

Method new()

Usage
idType$new(id)

Method .asXMLnodes()

Usage
idType$.asXMLnodes(node.name)

Method clone()

The objects of this class are cloneable with this method.

Usage
idType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

labelFormatType R6 class.

Description

Label used for pcrFormatType. Can take values:

ABC
123
A1a1

Inherits: enumType.

Format

An R6Class generator object.

Initialization

labelFormatType$new(value)

@section Fields:

value

checkString.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> labelFormatType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
labelFormatType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

lidOpenType R6 class.

Description

This step waits for the user to open the lid and continues afterwards. It allows to stop the program and to wait for the user to add for example enzymes and continue the program afterwards. The temperature of the previous step is maintained. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

lidOpenType$new()

Super class

RDML::rdmlBaseType -> lidOpenType

Methods

Public methods

Inherited methods

Method new()

Usage
lidOpenType$new()

Method clone()

The objects of this class are cloneable with this method.

Usage
lidOpenType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

loopType R6 class.

Description

This step allows to form a loop or to exclude some steps. It allows to jump to a certain "goto" step for "repeat" times. If the "goto" step is outside of the loop range, it must have "repeat" value "0". Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

loopType$new(goto, repeat.n)

Fields

goto

assertCount. The step to go to to form the loop.

repeat.n

assertCount. Determines how many times the loop is repeated. The first run through the loop is counted as 0, the last loop is "repeat" - 1.

Super class

RDML::rdmlBaseType -> loopType

Methods

Public methods

Inherited methods

Method new()

Usage
loopType$new(goto, repeat.n)

Method clone()

The objects of this class are cloneable with this method.

Usage
loopType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

mdpsType R6 class.

Description

Contains matrix of melting data points (single data points measured during amplification).

Format

An R6Class generator object.

Details

Columns:

tmp

(temperature in degrees Celsius at the time of measurement. Every point must have unique value.

fluor

fluorescence intensity measured without any correction (including baselining).

Inherits: rdmlBaseType.

Initialization

mdpsType$new(fpoints)

@section Fields:

fpoints

assertMatrix. Matrix with amplification data points.

Super class

RDML::rdmlBaseType -> mdpsType

Methods

Public methods

Inherited methods

Method new()

Usage
mdpsType$new(fpoints)

Method .asXMLnodes()

Usage
mdpsType$.asXMLnodes(node.name)

Method clone()

The objects of this class are cloneable with this method.

Usage
mdpsType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

measureType R6 class.

Description

Can take values:

real time
meltcurve

Inherits: enumType.

Format

An R6Class generator object.

Initialization

measureType$new(value)

@section Fields:

value

checkString.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> measureType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
measureType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Merges RDML objects

Description

Merges list of RDML objects. The first object in the list becomes base object. If experiments or runs have same name they will be combined. Reacts with same id, experiment and run overwrite each other!

Usage

MergeRDMLs(to.merge)

Arguments

to.merge

RDML objects that should be merged.

Examples

## Not run: 
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
lc96 <- RDML$new(filename)
filename <- paste(PATH, "/extdata/", "stepone_std.rdml", sep ="")
stepone <- RDML$new(filename)
merged <- MergeRDMLs(list(lc96,stepone))
merged$AsDendrogram()

## End(Not run)

Creates new instance of RDML class object

Description

This function has been designed to import data from RDML v1.1 and v1.2 format files or from xls file generated by Applied Biosystems 7500. To import from xls this file have to contain Sample Setup and Multicomponent Data sheets!

Arguments

filename

string – path to file
show.progress

logical – show loading progress bar if TRUE
conditions.sep

separator for condition defined at sample name
format

string – input file format. Possible values auto, rdml, abi, excel, csv. See Details.

Details

File format options:

auto

Tries to detect format by extension. .xlsx – excel, .xls – abi, .csv – csv, other – rdml

abi

Reads .xls files generated by ABI 7500 v.2. To create such files use File>Export; check 'Sample Setup' and 'Multicomponent Data'; select 'One File'

excel

.xls or .xslx file with sheets 'description', 'adp', 'mdp'. See example file table.xlsx

csv

.csv file with first column 'cyc' or 'tmp' and fluorescence data in other columns

rdml

.rdml or .lc96p files

Warning

Although the format RDML claimed as data exchange format, the specific implementation of the format at devices from real manufacturers differ significantly. Currently this function is checked against RDML data from devices: Bio-Rad CFX96, Roche LightCycler 96 and Applied Biosystems StepOne.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>, Stefan Roediger <[email protected]>, Michal Burdukiewicz <[email protected]>

Examples

## Not run: 
## Import from RDML file
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
lc96 <- RDML$new(filename)

## Some kind of overview for lc96
lc96$AsTable(name.pattern = sample[[react$sample$id]]$description)
lc96$AsDendrogram()

## End(Not run)

nucleotideType R6 class.

Description

Type of nucleic acid used as a template in the experiment. May have following values:

DNA
genomic DNA
cDNA
RNA

Format

An R6Class generator object.

Details

Inherits: enumType.

Initialization

nucleotideType$new(value)

@section Fields:

value

checkString. Value.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> nucleotideType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
nucleotideType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

oligoType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

oligoType$new(threePrimeTag = NULL,
  fivePrimeTag = NULL, sequence)

@section Fields:

threePrimeTag

checkString. Description of three prime modification (if present).

fivePrimeTag

checkString. Description of five prime modification (if present).

sequence

checkString.

Super class

RDML::rdmlBaseType -> oligoType

Methods

Public methods

Inherited methods

Method new()

Usage
oligoType$new(threePrimeTag = NULL, fivePrimeTag = NULL, sequence)

Method clone()

The objects of this class are cloneable with this method.

Usage
oligoType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

pauseType R6 class.

Description

This step allows to pause at a certain temperature. It is typically the last step in an amplification protocol. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

pauseType$new(temperature)

Fields

temperature

checkNumber. The temperature in degrees Celsius maintained during the pause.

Super class

RDML::rdmlBaseType -> pauseType

Methods

Public methods

Inherited methods

Method new()

Usage
pauseType$new(temperature)

Method clone()

The objects of this class are cloneable with this method.

Usage
pauseType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

pcrFormatType R6 class.

Description

The display format of the PCR, analogous to the the qPCR instrument run format. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Details

Rotor formats always have 1 column; rows correspond to the number of places in the rotor. Values for common formats are:

Format rows columns rowLabel columnLabel
single-well 1 1 123 123
48-well plate 6 8 ABC 123
96-well plate 8 12 ABC 123
384-well plate 16 24 ABC 123
1536-well plate 32 48 ABC 123
3072-well array 32 96 A1a1 A1a1
5184-well chip 72 72 ABC 123
32-well rotor 32 1 123 123
72-well rotor 72 1 123 123
100-well rotor 100 1 123 123
free format -1 1 123 123

If rows field has value -1, the function will not try to reconstruct a plate and just display all run data in a single column. If the columns field has value 1 then the function will not display a column label.

Initialization

pcrFormatType$new(rows, columns, rowLabel, columnLabel)

@section Fields:

rows

checkCount.

columns

checkCount.

rowLabel

labelFormatType.

columnLabel

labelFormatType.

Super class

RDML::rdmlBaseType -> pcrFormatType

Methods

Public methods

Inherited methods

Method new()

Usage
pcrFormatType$new(rows, columns, rowLabel, columnLabel)

Method clone()

The objects of this class are cloneable with this method.

Usage
pcrFormatType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

primingMethodType R6 class.

Description

The primers used in the reverse transcription. Can take values:

oligo-dt
random
target-specific
oligo-dt and random
other

Format

An R6Class generator object.

Details

Inherits: enumType.

Initialization

primingMethodType$new(value)

@section Fields:

value

checkString. Value.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> primingMethodType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
primingMethodType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

quantityType R6 class.

Description

A quantity is always defined by its value and its unit. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

quantityType$new(value, unit)

@section Fields:

value

checkNumber. Value.

unit

quantityUnitType. Unit.

Super class

RDML::rdmlBaseType -> quantityType

Methods

Public methods

Inherited methods

Method new()

Usage
quantityType$new(value, unit)

Method clone()

The objects of this class are cloneable with this method.

Usage
quantityType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

quantityUnitType R6 class.

Description

The unit the quantity. Can take values:

cop

copies per microliter

fold

fold change

dil

dilution (10 would mean 1:10 dilution)

nMol

nanomol per microliter

ng

nanogram per microliter

other

other unit (must be linear, no exponents or logarithms allowed)

Format

An R6Class generator object.

Details

Inherits: enumType.

Initialization

quantityUnitType$new(value)

@section Fields:

value

checkString. Value.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> quantityUnitType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
quantityUnitType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 class RDML – contains methods to read and overview fluorescence data from RDML v1.1 and v1.2 format files

Description

This class is a container for RDML format data (Lefever et al. 2009). The data may be further transformed to the appropriate format of the qpcR (Ritz et al. 2008, Spiess et al. 2008) and chipPCR (Roediger et al. 2015) packages (see RDML.new for import details). Real-time PCR Data Markup Language (RDML) is the recommended file format element in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (Bustin et al. 2009). The inner structure of imported data faithfully reflects the structure of RDML file v1.2. All data with the exception for fluorescence values can be represented as data.frame by method AsTable. Such possibility of data representation streamlines sample filtering (by targets, types, etc.) and serves as request for GetFData method, which extracts fluorescence data for specified samples.

Format

An R6Class generator object.

Fields

Type, structure of data and description of fields can be viewed at RDML v1.2 file description. Names of fields are first level of XML tree.

Methods

new

creates a new instance of RDML class object (see RDML.new)

AsTable

represent RDML data as data.frame (see RDML.AsTable)

GetFData

gets fluorescence data (see RDML.GetFData)

SetFData

sets fluorescence data (see RDML.SetFData)

Merge

merges two RDML to one (see MergeRDMLs)

AsDendrogram

represents structure of RDML object as dendrogram(see RDML.AsDendrogram)

Super class

RDML::rdmlBaseType -> RDML

Methods

Public methods

Inherited methods

Method AsDendrogram()

Usage
RDML$AsDendrogram(plot.dendrogram = TRUE)

Method AsTable()

Usage
RDML$AsTable(
  .default = list(exp.id = experiment$id$id, run.id = run$id$id, react.id = react$id$id,
    position = react$position, sample = react$sample$id, target = data$tar$id,
    target.dyeId = target[[data$tar$id]]$dyeId$id, sample.type =
    sample[[react$sample$id]]$type$value, adp = !is.null(data$adp), mdp =
    !is.null(data$mdp)),
  name.pattern = paste(react$position, react$sample$id,
    private$.sample[[react$sample$id]]$type$value, data$tar$id, sep = "_"),
  add.columns = list(),
  treat.null.as.na = FALSE,
  ...
)

Method GetFData()

Usage
RDML$GetFData(request, dp.type = "adp", long.table = FALSE)

Method AsXML()

Usage
RDML$AsXML(file.name)

Method SetFData()

Usage
RDML$SetFData(fdata, description, fdata.type = "adp")

Method new()

Usage
RDML$new(
  filename,
  show.progress = TRUE,
  conditions.sep = NULL,
  cluster = NULL,
  format = "auto"
)

Method clone()

The objects of this class are cloneable with this method.

Usage
RDML$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>, Stefan Roediger <[email protected]>, Michal Burdukiewicz <[email protected]>

References

RDML format http://www.rdml.org/ R6 package http://cran.r-project.org/web/packages/R6/index.html

qpcR package http://cran.r-project.org/web/packages/qpcR/index.html

chipPCR package: http://cran.r-project.org/web/packages/chipPCR/index.html

Roediger S, Burdukiewicz M and Schierack P (2015). chipPCR: an R Package to Pre-Process Raw Data of Amplification Curves. Bioinformatics first published online April 24, 2015 doi:10.1093/bioinformatics/btv205

Ritz, C., Spiess, A.-N., 2008. qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. Bioinformatics 24, 1549–1551. doi:10.1093/bioinformatics/btn227

Spiess, A.-N., Feig, C., Ritz, C., 2008. Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry. BMC Bioinformatics 9, 221. doi:10.1186/1471-2105-9-221

Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L., Vandesompele, J., Wittwer, C.T., 2009. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622. doi:10.1373/clinchem.2008.112797

Lefever, S., Hellemans, J., Pattyn, F., Przybylski, D.R., Taylor, C., Geurts, R., Untergasser, A., Vandesompele, J., RDML consortium, 2009. RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Res. 37, 2065–2069. doi:10.1093/nar/gkp056

Examples

## EXAMPLE 1:
## internal dataset lc96_bACTXY.rdml (in 'data' directory)
## generated by Roche LightCycler 96. Contains qPCR data
## with four targets and two types.
## Import with default settings.
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
lc96 <- RDML$new(filename)

tab <- lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,
                                         react$id$id), 
                    quantity = sample[[react$sample$id]]$quantity$value)
## Show dyes names
unique(tab$target.dyeId)
## Show types of the samples for dye 'FAM'
library(dplyr)
unique(filter(tab, target.dyeId == "FAM")$sample.type)

## Show template quantities for dye 'FAM' type 'std'#' 
## Not run: 
COPIES <- filter(tab, target.dyeId == "FAM", sample.type == "std")$quantity
## Define calibration curves (type of the samples - 'std').
## No replicates.
library(qpcR)
CAL <- modlist(lc96$GetFData(filter(tab,
                                    target.dyeId == "FAM", 
                                    sample.type == "std")),
               baseline="lin", basecyc=8:15)
## Define samples to predict (first two samples with the type - 'unkn').
PRED <- modlist(lc96$GetFData(filter(tab, 
                                    target.dyeId == "FAM", 
                                    sample.type == "unkn")),
               baseline="lin", basecyc=8:15)
## Conduct quantification.
calib(refcurve = CAL, predcurve = PRED, thresh = "cpD2",
      dil = COPIES)

## End(Not run)
## Not run: 
## EXAMPLE 2:
## internal dataset lc96_bACTXY.rdml (in 'data' directory)
## generated by Roche LightCycler 96. Contains qPCR data
## with four targets and two types.
## Import with default settings.
library(chipPCR)                        
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
lc96 <- RDML$new(filename)

tab <- lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,
                                         react$id$id), 
                    quantity = sample[[react$sample$id]]$quantity$value)
## Show targets names
unique(tab$target)
## Fetch cycle dependent fluorescence for HEX chanel
tmp <- lc96$GetFData(filter(tab, target == "bACT", sample.type == "std"))
## Fetch vector of dillutions 
dilution <- filter(tab, target.dyeId == "FAM", sample.type == "std")$quantity

## Use plotCurves function from the chipPCR package to 
## get an overview of the amplification curves
tmp <- as.data.frame(tmp)
plotCurves(tmp[,1], tmp[,-1])
par(mfrow = c(1,1))
## Use inder function from the chipPCR package to 
## calculate the Cq (second derivative maximum, SDM)
SDMout <- sapply(2L:ncol(tmp), function(i) {
  SDM <- summary(inder(tmp[, 1], tmp[, i]), print = FALSE)[2]
})

## Use the effcalc function from the chipPCR package and 
## plot the results for the calculation of the amplification
## efficiency analysis.
plot(effcalc(dilution, SDMout), CI = TRUE)

## End(Not run)
## Not run: 
## EXAMPLE 3:
## internal dataset BioRad_qPCR_melt.rdml (in 'data' directory)
## generated by Bio-Rad CFX96. Contains qPCR and melting data.
## Import with custom name pattern.
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
cfx96 <- RDML$new(filename)
## Use plotCurves function from the chipPCR package to 
## get an overview of the amplification curves
library(chipPCR)
## Extract all qPCR data 
tab <- cfx96$AsTable()
cfx96.qPCR <- as.data.frame(cfx96$GetFData(tab))
plotCurves(cfx96.qPCR[,1], cfx96.qPCR[,-1], type = "l")

## Extract all melting data 
cfx96.melt <- cfx96$GetFData(tab, dp.type = "mdp")
## Show some generated names for samples.
colnames(cfx96.melt)[2L:5]
## Select columns that contain
## samples with dye 'EvaGreen' and have type 'pos'
## using filtering by names.
cols <- cfx96$GetFData(filter(tab, grepl("pos_EvaGreen$", fdata.name)),
                       dp.type = "mdp")
## Conduct melting curve analysis.
library(qpcR)
invisible(meltcurve(cols, fluos = 2:ncol(cols),
          temps = rep(1, ncol(cols) - 1)))

## End(Not run)

Represents structure of RDML file as dendrogram

Description

Plots and/or returns the structure of RDML file as dendrogram (tree-like structure.)

Arguments

plot.dendrogram

plots dendrogram if TRUE

Value

dendrogram object

Author(s)

Konstantin A. Blagodatskikh <[email protected]>, Stefan Roediger <[email protected]>, Michal Burdukiewicz <[email protected]>

Examples

## Not run: 
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
cfx96 <- RDML$new(filename)
#plot dendrogram
cfx96$AsDendrogram()
#assign dendrogram to the object
dendr <- cfx96$AsDendrogram(plot.dendrogram = FALSE)

## End(Not run)

Represents fields of RDML object as data.frame

Description

Formats particular fields of RDML object as data.frames, filters or passes them to RDML.GetFData and RDML.SetFData functions.

Arguments

.default

list of default columns
name.pattern

expression to form fdata.name (see Examples)
add.columns

list of additional columns
treat.null.as.na

if value is NULL then convert it to NA. Helps to deal with incomplete records.
...

additional columns

Details

By default input this function forms data.frame with following columns:

exp.id

experiment$id

run.id

run$id

react.id

react$id

position

react$position

sample

react$sample

target

data$tar$id

target.dyeId

target[[data$id]]$dyeId

sample.type

sample[[react$sample]]$type

You can overload default columns list by parameter .default but note that columns 

exp.id, run.id, react.id, target

are necessary for usage AsTable output as input for GetFData and SetFData.
Additional columns can be introduced by specifying them at input parameter ... (see Examples). All default and additional columns accession expressions must be named.

Experiment, run, react and data to which belongs each fluorescence data vector can be accessed by experiment, run, react, data (see Examples).

Result table does not contain data from experiments with ids starting with '.'!

Author(s)

Konstantin A. Blagodatskikh <[email protected]>, Stefan Roediger <[email protected]>, Michal Burdukiewicz <[email protected]>

Examples

## Not run: 
## internal dataset stepone_std.rdml (in 'data' directory)
## generated by Applied Biosystems Step-One. Contains qPCR data.
library(chipPCR)
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "stepone_std.rdml", sep ="")
stepone <- RDML$new(filename)
## Mark fluorescense data which Cq > 30 and add quantities to
## AsTable output.
## Names for fluorescense data will contain sample name and react
## positions
tab <- stepone$AsTable(
         name.pattern = paste(react$sample$id, react$position),
         add.columns = list(cq30 = if(data$cq >= 30) ">=30" else "<30",
         quantity = sample[[react$sample$id]]$quantity$value)
         )
## Show cq30 and quantities
tab[, c("cq30", "quantity")]
## Get fluorescence values for 'std' type samples
## in format ready for ggplot function
library(dplyr)
fdata <- stepone$GetFData(
           filter(tab, sample.type == "std"),
           long.table = TRUE)
## Plot fdata with colour by cq30 and shape by quantity
library(ggplot2)
ggplot(fdata, aes(x = cyc, y = fluor,
                  group = fdata.name,
                  colour = cq30,
                  shape = as.factor(quantity))) +
                  geom_line() + geom_point()

## End(Not run)

Gets fluorescence data vectors from RDML object

Description

Gets fluorescence data vectors from RDML object for specified method of experiment.

Arguments

request

Output from AsTable method(RDML.AsTable)
dp.type

Type of fluorescence data (i.e. 'adp' for qPCR or 'mdp' for melting)
long.table

Output table is ready for ggplot (See RDML.AsTable for example)

Value

matrix which contains selected fluorescence data and additional information fromm request if long.table = TRUE.

Author(s)

Konstantin A. Blagodatskikh <[email protected]>, Stefan Roediger <[email protected]>, Michal Burdukiewicz <[email protected]>

Examples

## Not run: 
## internal dataset BioRad_qPCR_melt.rdml (in 'data' directory)
## generated by Bio-Rad CFX96. Contains qPCR and melting data.
## Import without splitting by targets/types and with
## custom name pattern.
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
cfx96 <- RDML$new(filename)
## Select melting fluorescence data with sample.type 'unkn'.
library(dplyr)
tab <- cfx96$AsTable()
fdata <- cfx96$GetFData(filter(tab, sample.type == "unkn"),
                        dp.type = "adp")
## Show names for obtained fdata
colnames(fdata)

## End(Not run)

Sets fluorescence data vectors to RDML object

Description

Sets fluorescence data vectors to RDML object for specified method of experiment.

Arguments

data

matrix containing in the first column data corresponding to all fluorescence values in the following columns. The name of the first column is the name of variable and names of other column are fdata.names (links to rows at description).
description

output from AsTable function that describes fluorescence data.
fdata.type

'adp' for qPCR, 'mdp' for melting data.

Examples

## Not run: 
PATH <- path.package("RDML")
filename <- paste0(PATH, "/extdata/", "stepone_std.rdml")
cfx96 <- RDML$new(filename)
## Use plotCurves function from the chipPCR package to 
## get an overview of the amplification curves
library(chipPCR)
## Extract all qPCR data 
tab <- cfx96$AsTable()
tab2 <- tab
tab2$run.id <- "cpp"
cfx96.qPCR <- as.data.frame(cfx96$GetFData(tab))
cpp <- cbind(cyc = cfx96.qPCR[, 1],
 apply(cfx96.qPCR[, -1], 2, 
   function(y) CPP(x = cfx96.qPCR[, 1], y = y)$y.norm))
cfx96$SetFData(cpp, tab2)
library(ggplot2)
library(gridExtra)
cfx96.gg <- cfx96$GetFData(tab, long.table = TRUE)
cpp.gg <- cfx96$GetFData(tab2,
                         long.table = TRUE)
plot1 <- ggplot(cfx96.gg, aes(x = cyc, y = fluor,
                group=fdata.name)) +
                 geom_line() +
                 ggtitle("Raw data")
plot2 <- ggplot(cpp.gg, aes(x = cyc, y = fluor,
                group=fdata.name)) +
                 geom_line() +
                 ggtitle("CPP processed data")
grid.arrange(plot1, plot2, nrow=2)

## End(Not run)

Base R6 class for RDML package.

Description

Most classes from RDML package inherit this class. It is designed for internal usage and should not be directly accessed.

Format

An R6Class generator object.

Initialization

rdmlBaseType$new()

Methods

.asXMLnodes(node.name)

Represents object as XML nodes. Should not be called directly. node.name – name of the root node for the generated XML tree.

print(...)

prints object

Methods

Public methods

Method .asXMLnodes()

Usage
rdmlBaseType$.asXMLnodes(node.name)

Method copy()

Usage
rdmlBaseType$copy()

Method print()

Usage
rdmlBaseType$print(...)

Method clone()

The objects of this class are cloneable with this method.

Usage
rdmlBaseType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

RDML Editor Graphical User Interface

Description

Launches graphical user interface that can edit RDML metadata and show qPCR or melting curves.

Usage

rdmlEdit()

rdmlIdType R6 class.

Description

This element can be used to assign a publisher and id to the RDML file.
Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

rdmlIdType$new(publisher, serialNumber,
  MD5Hash = NULL)

Fields

publisher

checkString. RDML file publisher.

serialNumber

checkString. Serial number.

MD5Hash

checkString. An MD5Hash calculated over the complete file after removing all rdmlIDTypes and all whitespaces between elements.

Super class

RDML::rdmlBaseType -> rdmlIdType

Methods

Public methods

Inherited methods

Method new()

Usage
rdmlIdType$new(publisher, serialNumber, MD5Hash = NULL)

Method clone()

The objects of this class are cloneable with this method.

Usage
rdmlIdType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

reactIdType R6 class.

Description

Contains identificator for reactType. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

reactIdType$new(id)

@section Fields:

id

checkCount. Identificator.

Super classes

RDML::rdmlBaseType -> RDML::idType -> reactIdType

Methods

Public methods

Inherited methods

Method new()

Usage
reactIdType$new(id)

Method clone()

The objects of this class are cloneable with this method.

Usage
reactIdType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

reactType R6 class.

Description

A reaction is an independent chemical reaction corresponding for example to a well in a 96 well plate, a capillary in a rotor, a through-hole on an array, etc. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Details

The ID of this reaction

Schemas :

  • rotor : assign IDs according to the position of the sample on the rotor (1 for the 1st sample, 2 for the 2nd, ...)

  • plate (96/384/1536 well) : the IDs are assigned in a row-first/column-second manner. For each row, the samples are numbered according to the increasing column number. At the end of a row, the numbering starts at the first column of the next row. An example for this type of plate can be found below :

    1 2 3 ...
    A 1 2 3
    B 13 14
    ...

    or

    1 2 3 ...
    1 1 2 3
    2 13 14
    ...

  • multi-array plate (BioTrove) : the IDs are assigned in a row-first/column-second manner, ignoring the organisation of sub-arrays. For each row, the samples are numbered according to the increasing column number. At the end of a row, the the next row. An example for this type of plate can be found below : todo...

Initialization

reactType$new(id, sample, data = NULL, pcrFormat = pcrFormatType$new(8, 12, labelFormatType$new("123"), labelFormatType$new("ABC")))

@section Fields:

id

reactIdType. See 'Details'.

sample

idReferencesType. SampleID - A reference to a sample.

data

list of dataType.

position

Human readable form of the react id (i.e. '13' -> 'B1')..

Methods

AsDataFrame(dp.type = "adp")

Represents amplification (dp.type = "adp") or melting (dp.type = "mdp") data points of all targets as one data.frame

.recalcPosition(pcrformat)

Converts react id to the human readable form (i.e. '13' -> 'B1'). This converted value can be accessed by position field. pcrFormat is pcrFormatType. Currently, only 'ABC' and '123' are supported as labels. For '123' '123' the Position will look like 'r01c01', for 'ABC' '123' it will be 'A01' and for '123' 'ABC' it will be 01A. 'ABC' 'ABC' is not currently supported. Note that 'ABC' will result in loss of information if the experiment contains more than 26 rows!

Super class

RDML::rdmlBaseType -> reactType

Methods

Public methods

Inherited methods

Method new()

Usage
reactType$new(
  id,
  sample,
  data = NULL,
  pcrFormat = pcrFormatType$new(8, 12, labelFormatType$new("ABC"),
    labelFormatType$new("123"))
)

Method GetFData()

Usage
reactType$GetFData(dp.type = "adp", long.table = FALSE)

Method .recalcPosition()

Usage
reactType$.recalcPosition(pcrFormat)

Method clone()

The objects of this class are cloneable with this method.

Usage
reactType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

runType R6 class.

Description

A run is a set of reactions performed in one "run", for example one plate, one rotor, one array, one chip. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

runType$new(id, description = NULL,
  documentation = NULL, experimenter = NULL, instrument = NULL,
  dataCollectionSoftware = NULL, backgroundDeterminationMethod = NULL,
  cqDetectionMethod = NULL, thermalCyclingConditions = NULL, pcrFormat,
  runDate = NULL, react = NULL)

Fields

id

idType.

description

checkString.

documentation

list of idReferencesType.

experimenter

list of idReferencesType.

instrument

checkString. Description of the instrument used to aquire the data.

dataCollectionSoftware

dataCollectionSoftwareType. Description of the software used to analyze/collect the data.

backgroundDeterminationMethod

checkString. Description of method used to determine the background.

cqDetectionMethod

cqDetectionMethodType. Description of method used to calculate the quantification cycle.

thermalCyclingConditions

idReferencesType. The program used to aquire the data.

pcrFormat

adpsType.

runDate

adpsType. Time stamp of data acquisition.

react

list of adpsType.

Methods

AsDataFrame(dp.type = "adp")

Represents amplification (dp.type = "adp") or melting (dp.type = "mdp") data points as data.frame

Super class

RDML::rdmlBaseType -> runType

Methods

Public methods

Inherited methods

Method new()

Usage
runType$new(
  id,
  description = NULL,
  documentation = NULL,
  experimenter = NULL,
  instrument = NULL,
  dataCollectionSoftware = NULL,
  backgroundDeterminationMethod = NULL,
  cqDetectionMethod = NULL,
  thermalCyclingConditions = NULL,
  pcrFormat,
  runDate = NULL,
  react = NULL
)

Method GetFData()

Usage
runType$GetFData(dp.type = "adp", long.table = FALSE)

Method UpdateReactsPosition()

Usage
runType$UpdateReactsPosition()

Method clone()

The objects of this class are cloneable with this method.

Usage
runType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

sampleType R6 class.

Description

A sample is a template solution with defined concentation. Since dilutions of the same material differ in concentration, they are considered different samples. A technical replicate samples should contain the same name (reactions are performed on the same material), and biological replicates should contain different names (the template derived from the different biological replicates is are divergent). Serial dilutions in a standard curve must have different names (preferably stating their dillution). Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

sampleType$new(id, description = NULL,
 documentation = NULL, xRef =  NULL, annotation = NULL, type =
 sampleTypeType$new("unkn"), interRunCalibrator = FALSE, quantity = NULL,
 calibratorSample = FALSE, cdnaSynthesisMethod = NULL, templateQuantity =
 NULL)

@section Fields:

id

idType. Concentration of the template in nanogram per microliter in the final reaction mix.

description

checkString.

documentation

list of idReferencesType.

xRef

list of xRefType.

annotation

list of annotationType.

type

sampleTypeType.

interRunCalibrator

checkFlag. TRUE if this sample is used as inter run calibrator.

quantity

quantityType. Quantity - The reference quantity of this sample. It should be only used if the sample is part of a standard curve. The provided value will be used to quantify unknown samples in absolute quantification assays. Only the use of positive integers (like 1, 10, 100, 1000) and fractions (e.g. 1, 0.1, 0.01, 0.001) is acceptable. The use of exponents (1, 2, 3, 4 or -1, -2, -3, -4) if forbidden, because it will not be interpreted as 10E1, 10E2, 10E3, 10E4 or 10E-1, 10E-2, 10E-3, 10E-4.

calibratorSample

checkFlag. TRUE if this sample is used as calibrator sample.

cdnaSynthesisMethod

cdnaSynthesisMethodType.

templateQuantity

templateQuantityType.

Super class

RDML::rdmlBaseType -> sampleType

Methods

Public methods

Inherited methods

Method new()

Usage
sampleType$new(
  id,
  description = NULL,
  documentation = NULL,
  xRef = NULL,
  annotation = NULL,
  type = sampleTypeType$new("unkn"),
  interRunCalibrator = FALSE,
  quantity = NULL,
  calibratorSample = FALSE,
  cdnaSynthesisMethod = NULL,
  templateQuantity = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
sampleType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

sampleTypeType R6 class.

Description

Can take values:

unkn

unknown sample

ntc

non template control

nac

no amplification control

std

standard sample

ntp

no target present

nrt

minusRT

pos

positive control

opt

optical calibrator sample

Format

An R6Class generator object.

Details

Inherits: enumType.

Initialization

sampleTypeType$new(value)

@section Fields:

value

checkString. Value.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> sampleTypeType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
sampleTypeType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

sequencesType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

sequencesType$new(forwardPrimer = NULL,
reversePrimer = NULL, probe1 = NULL, probe2 = NULL, amplicon = NULL)

@section Fields:

forwardPrimer

oligoType.

reversePrimer

oligoType.

probe1

oligoType.

probe2

oligoType.

amplicon

oligoType.

Super class

RDML::rdmlBaseType -> sequencesType

Methods

Public methods

Inherited methods

Method new()

Usage
sequencesType$new(
  forwardPrimer = NULL,
  reversePrimer = NULL,
  probe1 = NULL,
  probe2 = NULL,
  amplicon = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
sequencesType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

RDML$SetFData() wrapper

Description

Read more at RDML.SetFData

Usage

SetFData(obj, ...)

Arguments

obj

RDML object.
...

SetFData params.

stepType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

stepType$new(nr, description = NULL,
  temperature = NULL, gradient = NULL, loop = NULL, pause = NULL, lidOpen =
  NULL)

Fields

nr

checkCount. The incremental number of the step. First step should have value 1. The increment between steps should be constant and equivalent to 1.

description

checkString.

temperature

temperatureType.

gradient

gradientType.

loop

loopType.

pause

pauseType.

lidOpen

lidOpenType.

Super class

RDML::rdmlBaseType -> stepType

Methods

Public methods

Inherited methods

Method new()

Usage
stepType$new(
  nr,
  description = NULL,
  temperature = NULL,
  gradient = NULL,
  loop = NULL,
  pause = NULL,
  lidOpen = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
stepType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

targetType R6 class.

Description

A target is a PCR reaction with defined set of primers. PCR reactions for the same gene with distinct primer sequences are considered different targets. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

targetType$new(id, description = NULL,
  documentation = NULL, xRef = NULL, type, amplificationEfficiencyMethod =
  NULL, amplificationEfficiency = NULL, amplificationEfficiencySE = NULL,
  detectionLimit = NULL, dyeId, sequences = NULL, commercialAssay = NULL)

Fields

id

idType.

description

checkString.

documentation

list of idReferencesType.

xRef

list of xRefType.

type

targetTypeType.

amplificationEfficiencyMethod

checkString.

amplificationEfficiency

checkNumber.

amplificationEfficiencySE

checkNumber.

detectionLimit

checkNumber.

dyeId

idReferencesType.

sequences

sequencesType.

commercialAssay

commercialAssayType.

Super class

RDML::rdmlBaseType -> targetType

Methods

Public methods

Inherited methods

Method new()

Usage
targetType$new(
  id,
  description = NULL,
  documentation = NULL,
  xRef = NULL,
  type,
  amplificationEfficiencyMethod = NULL,
  amplificationEfficiency = NULL,
  amplificationEfficiencySE = NULL,
  detectionLimit = NULL,
  dyeId,
  sequences = NULL,
  commercialAssay = NULL
)

Method clone()

The objects of this class are cloneable with this method.

Usage
targetType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

targetTypeType R6 class.

Description

Can take values:

ref

reference target

toi

target of interest

Inherits: enumType.

Format

An R6Class generator object.

Initialization

targetTypeType$new(value)

@section Fields:

value

checkString.

Super classes

RDML::rdmlBaseType -> RDML::enumType -> targetTypeType

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
targetTypeType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

temperatureType R6 class.

Description

This step keeps a constant temperature on the heat block. Inherits: baseTemperatureType.

Format

An R6Class generator object.

Initialization

temperatureType$new(temperature, ...)

Fields

temperature

checkNumber. The temperature of the step in degrees Celsius.

...

Params of parent class baseTemperatureType.

Super classes

RDML::rdmlBaseType -> RDML::baseTemperatureType -> temperatureType

Methods

Public methods

Inherited methods

Method new()

Usage
temperatureType$new(temperature, ...)

Method clone()

The objects of this class are cloneable with this method.

Usage
temperatureType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

templateQuantityType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

templateQuantityType$new(conc, nucleotide)

@section Fields:

conc

checkNumber. Concentration of the template in nanogram

per microliter in the final reaction mix.

nucleotide

nucleotideType.

Super class

RDML::rdmlBaseType -> templateQuantityType

Methods

Public methods

Inherited methods

Method new()

Usage
templateQuantityType$new(conc, nucleotide)

Method clone()

The objects of this class are cloneable with this method.

Usage
templateQuantityType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

thermalCyclingConditionsType R6 class.

Description

A cycling program for PCR or to amplify cDNA. Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

thermalCyclingConditionsType$new(id,
  description = NULL, documentation = NULL, lidTemperature = NULL,
  experimenter = NULL, step)

Fields

id

idType.

description

checkString.

documentation

list of idReferencesType.

lidTemperature

checkNumber. The temperature in degrees Celsius of the lid during cycling.

experimenter

list of idReferencesType. Reference to the person who made or uses this protocol.

step

list of stepType. The steps a protocol runs through to amplify DNA.

Super class

RDML::rdmlBaseType -> thermalCyclingConditionsType

Methods

Public methods

Inherited methods

Method new()

Usage
thermalCyclingConditionsType$new(
  id,
  description = NULL,
  documentation = NULL,
  lidTemperature = NULL,
  experimenter = NULL,
  step
)

Method clone()

The objects of this class are cloneable with this method.

Usage
thermalCyclingConditionsType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

xRefType R6 class.

Description

Inherits: rdmlBaseType.

Format

An R6Class generator object.

Initialization

xRefType$new(name = NULL, id = NULL)

@section Fields:

name

checkString. Reference to an external database,

for example "GenBank".

id

checkString. The ID of the entry within the external database, for example "AJ832138".

Super class

RDML::rdmlBaseType -> xRefType

Methods

Public methods

Inherited methods

Method new()

Usage
xRefType$new(name = NULL, id = NULL)

Method clone()

The objects of this class are cloneable with this method.

Usage
xRefType$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.