gdcHeatmap {GDCRNATools} | R Documentation |
A heatmap showing unsupervised hierarchical clustering of
DE genes/miRNAs by heatmap.2
in the
gplots package
gdcHeatmap(deg.id, metadata, rna.expr)
deg.id |
a vector of Ensembl gene ids or miRBase v21 mature miRNA ids |
metadata |
metadata parsed from |
rna.expr |
|
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
Ruidong Li and Han Qu
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)