sapFinder (version 1.10.0)

easyRun: easyRun

Description

This function is used to automate the variation-associated database construction, MS/MS searching, post-processing and HTML-based report generation.

Usage

easyRun(vcf = NULL, annotation = NULL, refseq = NULL, outdir = "./", prefix = "sapFinder_test", spectra = "", cpu = 1, enzyme = "[KR]|[X]", tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", varmod = NULL, fixmod = NULL, miss = 2, maxCharge = 8, ti = FALSE, alignment = 1, xref = "noxref", xmx = NULL, ...)

Arguments

vcf

Input VCF file name. This file contains the information of gene sequence variations.

annotation

Input annotation file name. It contains the gene annotation information and can be downloaded from UCSC Genome Browser. Currently it supports RefSeq genes and ENSEMBL genes annotation file.

refseq

Input mRNA sequences file with FASTA format. It can be downloaded from UCSC Genome Browser.

outdir

Output directory.

prefix

The prefix of output file.

spectra

MS/MS peak list file

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.

alignment

0 or 1 to determine if peptide should be alignment or not. Default is 0.

xmx

The maximum Java heap size. The unit is "G".

xref

Optional external cross-reference file,generally it's downloaded through BioMart.If this file is provided,the final html report will present some relevant protein id or description.

...

Additional arguments

Examples

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")
mgf.path   <- system.file("extdata/sapFinder_test.mgf",
                            package="sapFinder")
xref       <- system.file("extdata/sapFinder_test_BioMart.Xref.txt",
                        package="sapFinder")
easyRun(vcf=vcf,annotation=annotation,refseq=refseq,outdir="test",
prefix="sapFinder_test",spectra=mgf.path,cpu=0,tol=10, tolu="ppm", itol=0.1,
itolu="Daltons",alignment=1,xref=xref)