Bibliospec_getScoreForPSM: Compute FDR and add it to RefSpectra Table

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

Description

Compute FDR and add it to RefSpectra Table

Examples

library(bibliospec)
library(prozor)

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

#call constructor
BS <- Bibliospec(dbfile=dbfile)
BS$listTables()
BS$annotateDB(fasta=file.path(path.package("bibliospec"),"extdata/uniprot.fasta.gz" ))
(specMeta <- BS$getSpectraMetaWithAnnotation())
specMeta <- BS$getSpectraMeta()

dim(specMeta)
specMeta
fdr <- prozor::computeFDR(specMeta$score, specMeta$proteinID,larger_better=FALSE)
head(fdr)

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