gdcDEReport {GDCRNATools} | R Documentation |
Report genes/miRNAs that are differentially expressed satisfying a given threshold
gdcDEReport(deg, gene.type = "all", fc = 2, pval = 0.01)
deg |
A dataframe of DE analysis result from
|
gene.type |
one of |
fc |
a numeric value specifying the threshold of fold change |
pval |
a nuemric value specifying the threshold of p value |
A dataframe or numeric matrix of differentially expressed genes/miRNAs
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-11', 'TCGA-2F-A9KT-11', 'TCGA-2F-A9KW-11') metaMatrix <- data.frame(sample_type=rep(c('PrimaryTumor', 'SolidTissueNormal'),each=3), sample=samples, days_to_death=seq(100,600,100), days_to_last_follow_up=rep(NA,6)) rnaMatrix <- matrix(c(6092,11652,5426,4383,3334,2656, 8436,2547,7943,3741,6302,13976, 1506,6467,5324,3651,1566,2780, 834,4623,10275,5639,6183,4548, 24702,43,1987,269,3322,2410, 2815,2089,3804,230,883,5415), 6,6) rownames(rnaMatrix) <- genes colnames(rnaMatrix) <- samples DEGAll <- gdcDEAnalysis(counts = rnaMatrix, group = metaMatrix$sample_type, comparison = 'PrimaryTumor-SolidTissueNormal', method = 'limma') dePC <- gdcDEReport(deg=DEGAll)