getImputedNAs_GeneSymbol_RnaSeq2: getImputedNAs_GeneSymbol_RnaSeq2

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

Description

Get a matrix of boolean values. A true in this matrix indicates that value is an NA which was added when the Gene Survey data was created.

Usage

getImputedNAs_GeneSymbol_RnaSeq2(theGeneEq,
theZipFile="/geneSurveyData/GeneSurvey.zip",
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 "/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.

Details

Get a matrix of boolean values. A true in this matrix indicates that value is an NA which was added when the Gene Survey data was created. This means the data should be interpreted as not measured or not reported rather than reported as an NA.

Value

Returns a matrix of values, with colnames being the sample ids (barcodes) and rownames the requested ids. 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.