Description Arguments Value Examples
get peptide anntotation list
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. |
list with psml - peptide spectrum match, modl - modification information, spectruml - the spectrum
1 2 3 4 5 6 7 8 9 10 11 12 | # 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)
|
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