gdcDEReport {GDCRNATools} | R Documentation

## Report differentially expressed genes/miRNAs

### 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)

[Package GDCRNATools version 1.10.1 Index]