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

!!!Caution work in progress!!!

Introduction

knitr::opts_chunk$set(echo = TRUE)

Create blib file from R

library(bibliospec)

datdir<-system.file("extdata", package = "bibliospec") 
tmp <- file.path(datdir,dir(datdir))
zip <- grep("*.zip",tmp,value=T)
print(zip)
unzip(zip ,exdir = datdir)
dat <- grep("*\\.dat",file.path(datdir,dir(datdir)),value=T)
BB <- Blib()
BB$build(dat , outfile = "test0_0.blib", cutoff=0.0 )

Initialize BS object

db <-file.path(path.package("bibliospec"),"extdata/peptideStd.sqlite")
BS <- Bibliospec(db)
BS$summary()

spectrMet <- BS$getSpectraMeta()
peaks <- BS$getPeaks()
dim(peaks)

Generate PSM set for specL compatibility

psmSet <- BS$getPsmSet()
psmSet[[1]]

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