gdcHeatmap: Heatmap of differentially expressed genes/miRNAs

In GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

A heatmap showing unsupervised hierarchical clustering of DE genes/miRNAs by heatmap.2 in the gplots package

Usage

gdcHeatmap(deg.id, metadata, rna.expr)

Arguments

deg.id	a vector of Ensembl gene ids or miRBase v21 mature miRNA ids
metadata	metadata parsed from gdcParseMetadata
rna.expr	voom transformed expression data

Value

A heatmap with rows are DE genes/miRNAs and columns are samples. Solid Tissue Normal samples are labeled with blue and Primary Tumor samples are labeled with red

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
gdcHeatmap(deg.id=genes, metadata=metaMatrix, rna.expr=rnaExpr)

GDCRNATools documentation built on Nov. 27, 2020, 2 a.m.