runTandem {sapFinder} | R Documentation

## 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")

[Package sapFinder version 1.18.0 Index]