RDML: 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) format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object.

Author
Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Date of publication
2015-07-22 06:08:46
Maintainer
Konstantin A. Blagodatskikh <k.blag@yandex.ru>
License
GPL (>= 2)
Version
0.9-1
URLs

View on CRAN

Man pages

adpsType
adpsType R6 class.
annotationType
annotationType R6 class.
AsDendrogram-function
'RDML$AsDendrogram()' wrapper
asdendrogram-method
Represents structure of 'RDML' file as dendrogram
astable-function
'RDML$AsTable()' wrapper
astable-method
Represents fields of 'RDML' object as 'data.frame'
baseTemperatureType
baseTemperatureType R6 class.
cdnaSynthesisMethodType
cdnaSynthesisMethodType R6 class.
commercialAssayType
commercialAssayType R6 class.
cqDetectionMethodType
cqDetectionMethodType R6 class.
dataCollectionSoftwareType
dataCollectionSoftwareType R6 class.
dataType
dataType R6 class.
documentationType
documentationType R6 class.
dyeType
dyeType R6 class.
enumType
enumType R6 class.
experimenterType
experimenterType R6 class.
experimentType
experimentType R6 class.
GetFData-function
'RDML$GetFData()' wrapper
getfdata-method
Gets fluorescence data vectors from 'RDML' object
gradientType
gradientType R6 class.
idReferencesType
idReferencesType R6 class.
idType
idType R6 class.
labelFormatType
labelFormatType R6 class.
lidOpenType
lidOpenType R6 class.
loopType
loopType R6 class.
mdpsType
mdpsType R6 class.
measureType
measureType R6 class.
MergeRDMLs
Merges 'RDML' objects
new-method
Creates new instance of 'RDML' class object
nucleotideType
nucleotideType R6 class.
oligoType
oligoType R6 class.
pauseType
pauseType R6 class.
pcrFormatType
pcrFormatType R6 class.
primingMethodType
primingMethodType R6 class.
quantityType
quantityType R6 class.
quantityUnitType
quantityUnitType R6 class.
RDML
R6 class 'RDML' - contains methods to read and overview...
rdmlBaseType
Base R6 class for RDML package.
rdmlIdType
rdmlIdType R6 class.
reactIdType
reactIdType R6 class.
reactType
reactType R6 class.
runType
runType R6 class.
sampleType
sampleType R6 class.
sampleTypeType
sampleTypeType R6 class.
sequencesType
sequencesType R6 class.
setfdata-function
'RDML$SetFData()' wrapper
setfdata-method
Sets fluorescence data vectors to 'RDML' object
stepType
stepType R6 class.
targetType
targetType R6 class.
targetTypeType
targetTypeType R6 class.
temperatureType
temperatureType R6 class.
templateQuantityType
templateQuantityType R6 class.
thermalCyclingConditionsType
thermalCyclingConditionsType R6 class.
xRefType
xRefType R6 class.

Files in this package

RDML
RDML/inst
RDML/inst/extdata
RDML/inst/extdata/BioRad_qPCR_melt.rdml
RDML/inst/extdata/stepone_std.rdml
RDML/inst/extdata/lc96_bACTXY.rdml
RDML/inst/doc
RDML/inst/doc/RDML.Rmd
RDML/inst/doc/RDML.R
RDML/inst/doc/RDML.html
RDML/NAMESPACE
RDML/CHANGELOG
RDML/R
RDML/R/RDML.types.R
RDML/R/RDML.GetFData.R
RDML/R/RDML.Merge.R
RDML/R/RDML.SetFData.R
RDML/R/RDML.AsTable.R
RDML/R/RDML.asserts.R
RDML/R/functional_wrappers.R
RDML/R/RDML.AsDendrogram.R
RDML/R/RDML.init.R
RDML/R/RDML.R
RDML/vignettes
RDML/vignettes/RDML_logo.png
RDML/vignettes/rdml_overview_1_2.png
RDML/vignettes/RDML.Rmd
RDML/README.md
RDML/MD5
RDML/build
RDML/build/vignette.rds
RDML/DESCRIPTION
RDML/man
RDML/man/reactType.Rd
RDML/man/rdmlBaseType.Rd
RDML/man/experimenterType.Rd
RDML/man/pcrFormatType.Rd
RDML/man/lidOpenType.Rd
RDML/man/adpsType.Rd
RDML/man/sampleTypeType.Rd
RDML/man/MergeRDMLs.Rd
RDML/man/targetTypeType.Rd
RDML/man/sequencesType.Rd
RDML/man/templateQuantityType.Rd
RDML/man/labelFormatType.Rd
RDML/man/mdpsType.Rd
RDML/man/idType.Rd
RDML/man/stepType.Rd
RDML/man/temperatureType.Rd
RDML/man/setfdata-function.Rd
RDML/man/measureType.Rd
RDML/man/enumType.Rd
RDML/man/runType.Rd
RDML/man/astable-function.Rd
RDML/man/nucleotideType.Rd
RDML/man/idReferencesType.Rd
RDML/man/dataType.Rd
RDML/man/dataCollectionSoftwareType.Rd
RDML/man/thermalCyclingConditionsType.Rd
RDML/man/baseTemperatureType.Rd
RDML/man/xRefType.Rd
RDML/man/dyeType.Rd
RDML/man/oligoType.Rd
RDML/man/sampleType.Rd
RDML/man/commercialAssayType.Rd
RDML/man/loopType.Rd
RDML/man/primingMethodType.Rd
RDML/man/getfdata-method.Rd
RDML/man/AsDendrogram-function.Rd
RDML/man/pauseType.Rd
RDML/man/gradientType.Rd
RDML/man/new-method.Rd
RDML/man/cdnaSynthesisMethodType.Rd
RDML/man/annotationType.Rd
RDML/man/setfdata-method.Rd
RDML/man/reactIdType.Rd
RDML/man/RDML.Rd
RDML/man/GetFData-function.Rd
RDML/man/documentationType.Rd
RDML/man/targetType.Rd
RDML/man/asdendrogram-method.Rd
RDML/man/astable-method.Rd
RDML/man/quantityUnitType.Rd
RDML/man/rdmlIdType.Rd
RDML/man/experimentType.Rd
RDML/man/cqDetectionMethodType.Rd
RDML/man/quantityType.Rd