evaluateDEA {pipeComp} | R Documentation |
Evaluates a differential expression analysis (DEA).
evaluateDEA(dea, truth = NULL, th = c(0.01, 0.05, 0.1))
dea |
Expects a data.frame with logFC and FDR, as produced by 'edgeR::topTags', 'limma::topTable' or 'DESeq2::results'. |
truth |
A data.frame containing the columns 'expected.beta' (real logFC) and 'isDE' (logical indicating whether there is a difference or not; accepts NA values) |
th |
The significance thresholds for which to compute the metrics. |
A list with two slots: 'logFC' (vector of metrics on logFC) and 'significance' table of significance-related statistics.
# fake DEA results dea <- data.frame( row.names=paste0("gene",1:10), logFC=rnorm(10) ) dea$PValue <- dea$FDR <- c(2:8/100, 0.2, 0.5, 1) truth <- data.frame( row.names=paste0("gene",1:10), expected.beta=rnorm(10), isDE=rep(c(TRUE,FALSE,TRUE,FALSE), c(3,1,2,4)) ) evaluateDEA(dea, truth)