diffExprStat {cTRAP} | R Documentation

## Differential expression's t-statistics sample

### Description

Differential expression's t-statistics sample obtained by running the following code:

    gene <- "EIF4G1"
    cellLine <- "HepG2"

    ENCODEmetadata <- downloadENCODEknockdownMetadata(cellLine, gene)
    table(ENCODEmetadata$`Experiment target`)
    length(unique(ENCODEmetadata$`Experiment target`))

    ENCODEsamples <- downloadENCODEsamples(ENCODEmetadata)
    counts <- prepareENCODEgeneExpression(ENCODEsamples)

    # Remove low coverage (at least 10 counts shared across two samples)
    minReads   <- 10
    minSamples <- 2
    filter <- rowSums(counts[ , -c(1, 2)] >= minReads) >= minSamples
    counts <- counts[filter, ]

    # Perform differential gene expression analysis
    diffExpr <- performDifferentialExpression(counts)

    # Get t-statistics of differential expression with respective gene names
    diffExprStat <- diffExpr$t
    names(diffExprStat) <- diffExpr$Gene_symbol

[Package cTRAP version 1.0.3 Index]