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 1.2.0 Index]