restab {pepStat} | R Documentation |
Tabulate the results of a peptide microarray analysis.
restab(peptideSet, calls)
peptideSet |
A |
calls |
A |
The peptideSet should be the one used in the function call to makeCalls
that generated the calls used. They should have identical peptides.
A data.frame
with the peptides and some information from the
peptideSet
as well as the frequency of binding for each group of the
calls.
## This example curated from the vignette -- please see vignette("pepStat") ## for more information if (require("pepDat")) { ## Get example GPR files + associated mapping file dirToParse <- system.file("extdata/gpr_samples", package = "pepDat") mapFile <- system.file("extdata/mapping.csv", package = "pepDat") ## Make a peptide set pSet <- makePeptideSet(files = NULL, path = dirToParse, mapping.file = mapFile, log=TRUE) ## Plot array images -- useful for quality control plotArrayImage(pSet, array.index = 1) plotArrayResiduals(pSet, array.index = 1, smooth = TRUE) ## Summarize peptides, using pep_hxb2 as the position database data(pep_hxb2) psSet <- summarizePeptides(pSet, summary = "mean", position = pep_hxb2) ## Normalize the peptide set pnSet <- normalizeArray(psSet) ## Smooth psmSet <- slidingMean(pnSet, width = 9) ## Make calls calls <- makeCalls(psmSet, freq = TRUE, group = "treatment", cutoff = .1, method = "FDR", verbose = TRUE) ## Produce a summary of the results summary <- restab(psmSet, calls) }