getDataMatrix_GeneSymbol_Meth450: getDataMatrix_GeneSymbol_Meth450

In MD-Anderson-Bioinformatics/GeneSurvey: MD Anderson Gene Survey

Description

Retrieves a matrix of values for all probes mapped to by the given gene symbol, with values for all samples/diseases.

Usage

getDataMatrix_GeneSymbol_Meth450(theGene,
theZipFile="/geneSurveyData/GeneSurvey.zip",
theRemoveDupFlag = TRUE, theVerboseFlag = FALSE, theUseDeltaFlag=FALSE)

Arguments

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

Value

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

Examples

#See examples in tests directory in the install.

MD-Anderson-Bioinformatics/GeneSurvey documentation built on May 7, 2019, 2:04 p.m.