parserGear {sapFinder} | R Documentation

## parserGear

### Description

This function is mainly for q-value calculation, protein inference and variant peptides spectra annotation.

### Usage

    parserGear(file = NULL, db = NULL, outdir = "parser_outdir",
      prefix = "sapFinder_test", mutPrefix = "VAR", decoyPrefix = "###REV###",
      alignment = 1, xmx = NULL, thread = 1)

### Arguments

`file` | MS/MS search file. Currently, only XML format file of X!Tandem and DAT result of Mascot are supported.
`db` | A FASTA format database file used for MS/MS searching. Usually, it is from the output of the function `dbCreator`.
`outdir` | Output directory.
`prefix` | The prefix of output file.
`mutPrefix` | The prefix of variant peptides ID. Default is "VAR". "VAR" is the prefix which used by function `dbCreator`.
`decoyPrefix` | The prefix of decoy sequences ID. Default is "###REV###". "###REV###" is the prefix which used by function `dbCreator`.
`alignment` | 0 or 1 to determine if peptide should be alignment or not. Default is 1.
`thread` | This parameter is used to specify the number of threads. "0" represents that all of the available threads are used; "1" represents one thread is used; "2" represents two threads are used,and so on. Default is 1.
`xmx` | The maximum Java heap size. The unit is "G".

### Examples

    ## Step 1. 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)

    ## Step 2. MS/MS searching
    mgf.path   <- system.file("extdata/sapFinder_test.mgf",
                                package="sapFinder")
    fasta.path <- db.files[1]
    xml.path   <- runTandem(spectra=mgf.path, fasta=fasta.path, outdir=".",
                            tol=10, tolu="ppm", itol=0.1, itolu="Daltons")

    ## Step 3. Post-processing
    parserGear(file=xml.path, db=fasta.path, prefix=prefix,
                outdir="parser_outdir", alignment=1)

[Package sapFinder version 1.25.0 Index]