Bibliospec_getAnnotationLists: get peptide anntotation list

Description Arguments Value Examples

Description

get peptide anntotation list

Arguments

excludeAA

Which AA to exclude - this argument is required because including amino acids with no mass defined will crash annotatePeaksWithFragments function, defualt is B, X and Z.

Value

list with psml - peptide spectrum match, modl - modification information, spectruml - the spectrum

Examples

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# use the sqlite file provided in the package
dbfile <- file.path(path.package("bibliospec"),
 "extdata/peptideStd.sqlite")

# call constructor
BS <- Bibliospec(dbfile=dbfile)
tmp <- BS$getAnnotationLists()
length(tmp$psml)
names(tmp)
tmp <- BS$getAnnotationLists(excludeAA = "Y|R")
length(tmp$psml)
stopifnot(length(tmp$psml) == 44)

protViz/bibliospec documentation built on May 26, 2019, 9:37 a.m.