R/analyzeDeepn.R

In pbreheny/deepn: Dynamic Enrichment for Evaluation of Protein Networks

analyzeDeepn <- function(infile, outfile="stat.csv", msgfile="messages.txt", debug=FALSE, sort=1) {
  Data <- importFromDeepn(infile)
  Data$omega <- overdisp(Data)
  out <- c("Overdispersion estimates",
           paste("Baseline (vector only):   ", formatC(Data$omega["Baseline"], digits=2, format="f")),
           paste("Baseline (vector + bait): ", formatC(Data$omega["baitEffect"], digits=2, format="f")),
           paste("Selection:                ", formatC(Data$omega["Selected"], digits=2, format="f")),
           "-----",
           "Baseline overdispersions should be around 0 (no overdispersion)",
           "Overdispersion under selection conditions will ideally be under 2.")
  if (Data$omega["baitEffect"] > 2*Data$omega["Baseline"] & Data$omega["baitEffect"] > .15) {
    out <- c(out, "", "WARNING: There appears to be evidence of secondary bait effects.",
             "Abundances in presence of bait are different from abundances in absence of",
             "bait, even under non-selective conditions.  This generally indicates that",
             "the bait is disrupting growth or sequencing in unintended ways.")
  }
  writeLines(out, msgfile)
  
  if (debug) Data <- applyFilter(Data, thresh=500)
  fit <- runMCMC(Data)
  object <- psm(fit)
  summary(object, sort=sort, allGenes=TRUE, outfile=outfile)
}