Description Arguments Examples
annotate spectrum
psm |
peptide spectrum match table |
modification |
modification table |
spectrum |
spectrum table |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | library(bibliospec)
rm(list=ls())
dbfile <- file.path(path.package("bibliospec"),
"extdata/peptideStd.sqlite")
# call constructor
BS <- Bibliospec(dbfile=dbfile)
tmp <- BS$getAnnotationLists()
names(tmp)
tmp$psml[[1]]
tmp$mod[[1]]
tmp$spectruml[[1]]
ann <- Annotate()
ann$aa2mass(tmp$psml[[1]]$peptideSeq)
spectrum <- tmp$spectruml[[1]]$mz
masses <- ann$aa2mass(tmp$psm[[1]]$peptideSeq)
xx<-ann$fragmentBYIonsUpTO( masses , charge = (tmp$psm[[1]]$precursorCharge -1))
head(xx)
x<-ann$psmEasy(spectrum, xx$mass )
head(x)
matches <- ann$annotateSpectrum(psm = tmp$psml[[1]],
modification = tmp$modl[[1]], spectrum = tmp$spectruml[[1]])
head(matches)
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