parserGear: parserGear

In sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.

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)

sapFinder documentation built on Nov. 8, 2020, 5:59 p.m.