gdcDEReport: Report differentially expressed genes/miRNAs

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

Description

Report genes/miRNAs that are differentially expressed satisfying a given threshold

Usage

gdcDEReport(deg, gene.type = "all", fc = 2, pval = 0.01)

Arguments

deg	A dataframe of DE analysis result from gdcDEAnalysis
gene.type	one of 'all', 'long_non_coding', 'protein_coding', and 'miRNAs'. Default is 'all'
fc	a numeric value specifying the threshold of fold change
pval	a nuemric value specifying the threshold of p value

Value

A dataframe or numeric matrix of differentially expressed genes/miRNAs

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-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)

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.