runTandem: run X!Tandem

In Shawn-Xu/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

Description

run X!Tandem

Usage

runTandem(spectra = "", fasta = "", outdir = ".", cpu = 1,
  enzyme = "[KR]|[X]", tol = 10, tolu = "ppm", itol = 0.6,
  itolu = "Daltons", varmod = NULL, fixmod = NULL, miss = 2,
  maxCharge = 8, ti = FALSE)

Arguments

spectra	MS/MS peak list file
fasta	Protein database file for searching.
outdir	The output directory.
cpu	The number of CPU used for X!Tandem search. Default is 1.
enzyme	Specification of specific protein cleavage sites. Default is "[KR]|[X]".
tol	Parent ion mass tolerance (monoisotopic mass).
tolu	Parent ion M+H mass tolerance window units.
itol	Fragment ion mass tolerance (monoisotopic mass).
itolu	Unit for fragment ion mass tolerance (monoisotopic mass).
varmod	Specificiation of potential modifications of residues.
fixmod	Specification of modifications of residues.
miss	The number of missed cleavage sites. Default is 2.
maxCharge	The Maximum parent charge, default is 8
ti	anticipate carbon isotope parent ion assignment errors. Default is false.

Value

The search result file path

Examples

vcffile <- system.file("extdata/input", "PGA.vcf",package="PGA")
bedfile <- system.file("extdata/input", "junctions.bed",package="PGA")
gtffile <- system.file("extdata/input", "transcripts.gtf",package="PGA")
annotation <- system.file("extdata", "annotation",package="PGA")
outfile_path<-"db/"
outfile_name<-"test"
library(BSgenome.Hsapiens.UCSC.hg19)
dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,
                    annotation_path=annotation,outfile_name=outfile_name,
                    genome=Hsapiens,outdir=outfile_path)

msfile <- system.file("extdata/input", "pga.mgf",package="PGA")
runTandem(spectra = msfile, fasta = dbfile, outdir = "./", cpu = 6,
          enzyme = "[KR]|[X]", varmod = "15.994915@M",
          fixmod = "57.021464@C", tol = 10, tolu = "ppm", itol = 0.05,
          itolu = "Daltons", miss = 2, maxCharge = 8, ti = FALSE)

Shawn-Xu/PGA documentation built on Aug. 28, 2020, 9:58 p.m.