easyRun {sapFinder} | R Documentation |
This function is used to automate the variation-associated database construction, MS/MS searching, post-processing and HTML-based report generation.
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, ...)
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 |
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)