reportGear {PGA} | R Documentation

## The main function for report generation

### Description

The main function for report generation

### Usage

    reportGear(parser_dir, tab_dir, report_dir)

### Arguments

`parser_dir` | The directory which contains the peptide identification results
`tab_dir` | The directory which contains the database annotation files
`report_dir` | The report output directory

### Value

none

### Examples

    vcffile <- system.file("extdata/input", "PGA.vcf",package="PGA")
    bedfile <- system.file("extdata/input", "junctions.bed",package="PGA")
    gtffile <- system.file("extdata/input", "transcripts.gtf",package="PGA")
    annotation <- system.file("extdata", "annotation",package="PGA")
    outfile_path<-"db/"
    outfile_name<-"test"
    library(BSgenome.Hsapiens.UCSC.hg19)
    dbfile <- dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,
                        annotation_path=annotation,outfile_name=outfile_name,
                        genome=Hsapiens,outdir=outfile_path)

    msfile <- system.file("extdata/input", "pga.mgf",package="PGA")
    idfile <- runTandem(spectra = msfile, fasta = dbfile, outdir = "./", cpu = 6,
                        enzyme = "[KR]|[X]", varmod = "15.994915@M",itol = 0.05,
                        fixmod = "57.021464@C", tol = 10, tolu = "ppm",
                        itolu = "Daltons", miss = 2, maxCharge = 8, ti = FALSE)
    parserGear(file = idfile, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=8,
               outdir = "parser_outdir")
    reportGear(parser_dir = "parser_outdir", tab_dir = outfile_path,
               report_dir = "report")

[Package PGA version 1.8.1 Index]