runTandem: run xtandem

In sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.

Description

run xtandem

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]".
varmod	Specificiation of potential modifications of residues.
fixmod	Specification of modifications of residues.
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).
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

# Variation-associated database construction
vcf        <- system.file("extdata/sapFinder_test.vcf",
                        package="sapFinder")
annotation <- system.file("extdata/sapFinder_test_ensGene.txt",
                        package="sapFinder")
refseq     <- system.file("extdata/sapFinder_test_ensGeneMrna.fa",
                        package="sapFinder")
xref       <- system.file("extdata/sapFinder_test_BioMart.Xref.txt",
                        package="sapFinder")
outdir     <- "db_dir"
prefix     <- "sapFinder_test"
db.files <- dbCreator(vcf=vcf, annotation=annotation,
                refseq=refseq, outdir=outdir,
                prefix=prefix,xref=xref)

# MS/MS searching
mgf.path   <- system.file("extdata/sapFinder_test.mgf",
                            package="sapFinder")
runTandem(spectra=mgf.path,fasta=db.files[1],
        tol=10,tolu="ppm",itol=0.1,itolu="Daltons")

sapFinder documentation built on Nov. 8, 2020, 5:59 p.m.