getData_CombinedHsaMimat_miRNASeq: getData_CombinedHsaMimat_miRNASeq
In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description Usage Arguments Value Examples

Retrieves a list of values for all samples/diseases for the given combined HSA and MIMAT id.

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

`theGeneEq`	A vector of combined HSA and MIMAT id names as found in the getNames_ function for this data type. This consists of ids similar to "hsa-mir-663.MIMAT0003326" and "hsa-mir-663b.MIMAT0005867". This means a single HSA format id can have multiple entries (MIMAT ids).
`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.

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