runTandem {PGA} | R Documentation

## run X!Tandem

### 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)

[Package PGA version 1.14.0 Index]