evaluateDensities {SPsimSeq} | R Documentation |
Evaluate the densities in the estimated SPsimSeq object
evaluateDensities(SPobj, newData = names(SPobj$detailed.results$densList))
SPobj |
The SPsimSeq object, with details retained |
newData |
A character vector of gene names |
a list of estimated densities, breaks and midpoints, one for every gene in newData
data("zhang.data.sub") # filter genes with sufficient expression (important step to avoid bugs) zhang.counts <- zhang.data.sub$counts MYCN.status <- zhang.data.sub$MYCN.status # simulate data sim.data.bulk <- SPsimSeq(n.sim = 1, s.data = zhang.counts, group = MYCN.status, n.genes = 2000, batch.config = 1, group.config = c(0.5, 0.5), tot.samples = 20, pDE = 0.1, lfc.thrld = 0.5, result.format = "list", return.details = TRUE) outDens = evaluateDensities(sim.data.bulk) select.genes <- sample(names(outDens), 4) select.sample = sample( seq_along(sim.data.bulk$detailed.results$exprmt.design$sub.groups), 1) par(mfrow=c(2, 2)) for(i in select.genes){ plot(outDens[[i]][[select.sample]]$mids, outDens[[i]][[select.sample]]$gy, type = "l", xlab = "Outcome", ylab = "Density", main = paste("Gene", i)) }