summarizePeptides {pepStat} | R Documentation |
This function merges the replicates and adds information from a peptide collection to a peptideSet. This collection can include coordinates, alignment information, Z-scales, and other peptide information.
summarizePeptides(peptideSet, summary = "median", position = NULL)
peptideSet |
A |
summary |
A |
position |
A |
The object in the position argument will be passed to create_db
, it
can either be a GRanges
object with a peptide as a metadata column, or
a data.frame
that can be used to create such GRanges
.
Some peptide collections can be found in the pepDat
package.
An object of class peptideSet
with added columns and updated ranges.
Raphael Gottardo, Greory Imholte
makePeptideSet
, create_db
,
create_db
## 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) }