gdcMatchSamples {GDCRNATools}R Documentation

Match samples in metadata and expression matrix

Description

Check if samples in the metadata and expression data match

Usage

gdcMatchSamples(metadata, rna.expr)

Arguments

metadata

metadata parsed from gdcParseMetadata

rna.expr

voom transformed expression data

Value

A logical value. If TRUE, all the samples matched

Author(s)

Ruidong Li and Han Qu

Examples

genes <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
        'ENSG00000001084','ENSG00000001167','ENSG00000001460')

samples <- c('TCGA-2F-A9KO-01', 'TCGA-2F-A9KP-01',
            'TCGA-2F-A9KQ-01', 'TCGA-2F-A9KR-01',
            'TCGA-2F-A9KT-01', 'TCGA-2F-A9KW-01')
             
metaMatrix <- data.frame(sample_type=rep('PrimaryTumor',6),
                        sample=samples,
                        days_to_death=seq(100,600,100),
                        days_to_last_follow_up=rep(NA,6))
rnaExpr <- matrix(c(2.7,7.0,4.9,6.9,4.6,2.5,
                    0.5,2.5,5.7,6.5,4.9,3.8,
                    2.1,2.9,5.9,5.7,4.5,3.5,
                    2.7,5.9,4.5,5.8,5.2,3.0,
                    2.5,2.2,5.3,4.4,4.4,2.9,
                    2.4,3.8,6.2,3.8,3.8,4.2),6,6)
rownames(rnaExpr) <- genes
colnames(rnaExpr) <- samples
gdcMatchSamples(metadata=metaMatrix, rna.expr=rnaExpr)

[Package GDCRNATools version 1.4.1 Index]