sapFinder (version 1.10.0)

runTandem: run xtandem

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")