Bibliospec_annotateDB: Annotate naked peptide seqeuences with protein IDs using...

In protViz/bibliospec: Reading and Analyzing Mass Spectrometric Search Results

Description

Annotate naked peptide seqeuences with protein IDs using fasta file and creates table PeptideAnnotation

Arguments

fasta

fasta file either a list generated using prozor::readPeptideFasta or a path to a fasta file

Value

table with annotated peptides

Examples

library(bibliospec)
dbfile <- file.path(path.package("bibliospec"),  "extdata/peptideStd.sqlite")

# call constructor
BS <- Bibliospec(dbfile=dbfile)
BS$listTables()
library(prozor)
human <- prozor::readPeptideFasta(file=file.path(path.package("bibliospec"),"extdata/uniprot.fasta.gz" ))
tmp <- BS$annotateDB(fasta=c(human))

mods <- BS$sql("select * from PeptideAnnotation" )

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