getDataObject_GeneSymbol_Meth27: getDataObject_GeneSymbol_Meth27

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

Returns an R object with the data for the requested vector, and annotations for samples, genome, and diseases.

Usage

getDataObject_GeneSymbol_Meth27(theGeneList, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theRemoveDupFlag = TRUE, theVerboseFlag = FALSE, theRDataFile = NULL, theListOnlyFlag=FALSE, theUseDeltaFlag=FALSE)

Arguments

theGeneList	A vector of gene symbol names as found in the getNames_ function for this data type.
theZipFile	Default: For DQS Servers. If you are on a server where the GENE_REPORT directory is on a different path, you can pass in a value to override the default of "/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip".
theRemoveDupFlag	Default: FALSE. Remove the duplicate barcodes from the same control samples used in different diseases.
theVerboseFlag	Default: FALSE. TRUE means write all output, which can be very verbose.
theRDataFile	Default: NULL. If non null, uses this value as a full path, including filename, to write a file with the given object.
theListOnlyFlag	Default: FALSE. If TRUE, save the RData file as a list with elements matching the object slots, so it can be shared with people who do not have the package.
theUseDeltaFlag	Default: FALSE. A flag indicating to use the differences in value between tumor and normal samples.

Value

The return value is an object. The following functions work to pull data out of the object.

get.Data	get.Data
get.GenomeAnnotations	get.GenomeAnnotations
get.SampleAnnotations	get.SampleAnnotations
get.TissueAnnotations	get.TissueAnnotations

Examples

#getDataObject_GeneSymbol_Meth27(getNames_GeneSymbol_Meth27()[c(1,100)])

GeneSurvey/TCGAGeneReport documentation built on May 6, 2019, 6:27 p.m.