RDML v0.9-8

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Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

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.

Readme

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RDML

The RDML package is published in Oxford Bioinformatics: Stefan Rödiger, Michał Burdukiewicz, Andrej-Nikolai Spiess, Konstantin Blagodatskikh; Enabling reproducible real-time quantitative PCR research: the RDML package, Bioinformatics, https://doi.org/10.1093/bioinformatics/btx528 (see also citation()).

Imports qPCR data from RDML v1.1 format files (Lefever et al. 2009) and transforms it to the appropriate format of the qpcR package (Ritz et al. 2008, Spiess et al. 2008) or chipPCR package. RDML (Real-time PCR Data Markup Language) is the recommended file format element in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (Bustin et al. 2009).

Installation


The stable version of the RDML package for R is hosted on CRAN and can be installed as any R package.

You can install the latest development version of the code using the devtools R package.

# Install devtools, if you haven't already.
install.packages("devtools")

library(devtools)
install_github("kablag/RDML")

Manual

The manual is available online.

Examples

RDML imports various data formats (CSV, XMLX) besides the RDML format. Provided that the raw data have a defined structure (as described in the vignette) the import should be done by a few clicks. The example below shows the import of amplification curve data, which were stored in a CSV file. The function rdmlEdit() was used in the RKWard IDE/GUI for further processing. rdmlEdit may be also accessed as a web server (http://shtest.evrogen.net/rdmlEdit/).

Data Import

Once imported enables rdmlEdit() and other functions from the RDML package complex data visualization and processing in the R statistical computing environment.

Data View

Functions in RDML

Name Description
MergeRDMLs Merges RDML objects
RDML R6 class RDML -- contains methods to read and overview fluorescence data from RDML v1.1 and v1.2 format files
AsDendrogram RDML$AsDendrogram() wrapper
GetFData RDML$GetFData() wrapper
RDML.AsDendrogram Represents structure of RDML file as dendrogram
AsTable RDML$AsTable() wrapper
as.character.idType Convert idType object to character
as.character.reactIdType Convert reactIdType object to character
adpsType adpsType R6 class.
annotationType annotationType R6 class.
RDML.AsTable Represents fields of RDML object as data.frame
baseTemperatureType baseTemperatureType R6 class.
lidOpenType lidOpenType R6 class.
cdnaSynthesisMethodType cdnaSynthesisMethodType R6 class.
commercialAssayType commercialAssayType R6 class.
idType idType R6 class.
labelFormatType labelFormatType R6 class.
pcrFormatType pcrFormatType R6 class.
primingMethodType primingMethodType R6 class.
sampleType sampleType R6 class.
cqDetectionMethodType cqDetectionMethodType R6 class.
dataCollectionSoftwareType dataCollectionSoftwareType R6 class.
experimentType experimentType R6 class.
loopType loopType R6 class.
mdpsType mdpsType R6 class.
measureType measureType R6 class.
rdmlBaseType Base R6 class for RDML package.
rdmlEdit RDML Editor Graphical User Interface
dataType dataType R6 class.
documentationType documentationType R6 class.
gradientType gradientType R6 class.
idReferencesType idReferencesType R6 class.
RDML.SetFData Sets fluorescence data vectors to RDML object
stepType stepType R6 class.
dyeType dyeType R6 class.
enumType enumType R6 class.
[.GetFData Extract data points from RDML object
RDML.GetFData Gets fluorescence data vectors from RDML object
oligoType oligoType R6 class.
sampleTypeType sampleTypeType R6 class.
targetType targetType R6 class.
targetTypeType targetTypeType R6 class.
new Creates new instance of RDML class object
nucleotideType nucleotideType R6 class.
sequencesType sequencesType R6 class.
SetFData RDML$SetFData() wrapper
pauseType pauseType R6 class.
reactType reactType R6 class.
runType runType R6 class.
temperatureType temperatureType R6 class.
experimenterType experimenterType R6 class.
quantityType quantityType R6 class.
quantityUnitType quantityUnitType R6 class.
rdmlIdType rdmlIdType R6 class.
reactIdType reactIdType R6 class.
thermalCyclingConditionsType thermalCyclingConditionsType R6 class.
xRefType xRefType R6 class.
templateQuantityType templateQuantityType R6 class.
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Vignettes of RDML

Name
CreateRDML.Rmd
File_import.png
RDML.Rmd
RDML.bib
RDML_logo.png
bench_df.csv
data_view.png
rdml_overview_1_2.png
usingRDML_with_other_R_packages.Rmd
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Details

Type Package
LazyData true
Date 2017-09-05
License MIT + file LICENSE
URL https://github.com/kablag/RDML
Collate 'RDML.types.R' 'RDML.R' 'RDML.AsDendrogram.R' 'RDML.AsTable.R' 'RDML.GetFData.R' 'RDML.Merge.R' 'RDML.SetFData.R' 'RDML.init.R' 'functional_wrappers.R' 'rdmlEdit.R'
VignetteBuilder knitr
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-09-05 08:44:17 UTC; elf
Repository CRAN
Date/Publication 2017-09-05 09:05:36 UTC

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