easyRun {sapFinder} | R Documentation

## 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)

[Package sapFinder version 1.18.0 Index]