runTandem {proteoQC} | R Documentation

## Run X!Tandem

### Description

Run X!Tandem

run X!Tandem

### Usage

    runTandem(spectra = "", fasta = "", outdir = "./", outprefix = "",
      cpu = 1, enzyme = 1, xmx = 2, varmod = NULL, fixmod = NULL,
      refine = TRUE, ntt = 1, tol = 10, tolu = "ppm", itol = 0.6,
      itolu = "Daltons", miss = 1)

### Arguments

`spectra` | MS/MS peak list file
`fasta` | database file
`outdir` | output directory
`outprefix` | output file prefix
`cpu` | The number of CPU used for X!Tandem
`enzyme` | The ID of enzyme used for database searching. See `showEnzyme`.
`xmx` | Set for parameter of "Java -Xmx".
`varmod` | Variable modifications used for database searching. See `showMods`.
`fixmod` | Fixed modifications used for database searching. See `showMods`.
`refine` | Refine search, default is TRUE
`ntt` | Default is 1
`tol` | The error window on experimental peptide mass values
`tolu` | Units can be selected from: ppm, Daltons.
`itol` | Error window for MS/MS fragment ion mass values.
`itolu` | Units can be selected from: Daltons
`miss` | Max miss clevage

### Value

a file path

### Author(s)

Bo Wen wenbo@genomics.cn

[Package proteoQC version 1.18.1 Index]