diffExprStat {cTRAP} | R Documentation |
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