filterForCommonSamples: filterForCommonSamples

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

The filterForCommonSamples function does not need a path itself. You can pass it what ever getData_ results you would like. The getData_ vectors are returned within a list, filtered down to only common samples, using the first 15 characters of the TCGA sample id. (15 characters are used so tumor samples and normal are still distinguished.)

Usage

filterForCommonSamples(...)

Arguments

...

Details

The filterForCommonSamples function does not need a path itself. You can pass it what ever readGene results you would like. The getData_ vectors are returned within a list, filtered down to only common samples, using the first 15 characters of the TCGA sample id. (15 characters are used so tumor samples and normal are still distinguished.)

foo<-filterForCommonSamples(getData_GeneSymbol_RnaSeq2("TP53"), getData_GeneSymbol_RnaSeq("TP53")) > foo[[1]][1:5] TCGA-BL-A0C8-01 TCGA-BL-A13I-01 TCGA-BL-A13J-01 TCGA-BL-A13J-11 TCGA-BT-A0S7-01 10.347709 11.158277 10.923567 9.501043 12.141164 > foo[[2]][1:5] TCGA-BL-A0C8-01 TCGA-BL-A13I-01 TCGA-BL-A13J-01 TCGA-BL-A13J-11 TCGA-BT-A0S7-01 5.193636 6.211073 5.821068 4.205293 6.926390

Value

A list containing vectors filtered down to only common samples, using the first 15 characters of the TCGA sample id.

Examples

#filterForCommonSamples(getData_GeneSymbol_RnaSeq2("TP53"), getData_GeneSymbol_RnaSeq("TP53"))

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