analyzeDuplicated: analyse duplicated peptides/proteins

In wolski/imsbInfer: Visualization, normalization and QC of proteomics SWATH-MS data

Description

analyse duplicated peptides/proteins

Usage

analyzeDuplicated(data, dups, maxpep = 3, countmax = 1000,
  method = "spearman")

Arguments

data	- msExperiment
dups	- list as returned by function getListOfDuplicated
maxpep	- limit the number of duplicated peptides
countmax	- limit the total number of comparisons
method	- type of correlation to compute

See Also

getListOfDuplicated analyzeDuplicatedPeptides

Examples

data(SDat)
rownames = SDat$pepinfo$PeptideSequence
dups = getListOfDuplicated(rownames)

res = analyzeDuplicated(SDat , dups[1:25])
dim(res)
res[1,]
hist(res$cor)
plot(res$medianRTDiff,res$cor)

rownames = SDat$pepinfo$PeptideSequence
nondups = getUniqueEntries(rownames)
length(nondups)
if(length(nondups > 0)){
 res = analyzeDuplicated(SDat , list(nondups[1:25]))
}

wolski/imsbInfer documentation built on March 27, 2021, 11:39 p.m.