getData_GeneSymbol_SNP6: getData_GeneSymbol_SNP6

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

Retrieves a list of values for all samples/diseases for the given gene symbol.

Usage

getData_GeneSymbol_SNP6(theGeneEq, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theUseDeltaFlag = FALSE, theRemoveDupFlag = TRUE, theVerboseFlag = FALSE)

Arguments

theGeneEq	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".
theUseDeltaFlag	Default: FALSE. A flag indicating to use the differences in value between tumor and normal samples.
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.

Value

Returns a matrix of values, with colnames being the sample ids (barcodes) and rownames the gene symbols. Samples and row ids are in sorted order, not requested order.

Examples

#getData_Probe_SNP6(getNames_GeneSymbol_SNP6()[1])

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