easyRun: easyRun

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

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)

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