| runTandem {sapFinder} | R Documentation |
run xtandem
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)
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. |
The search result file path
# 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")