reportCreator {sapFinder} | R Documentation

## reportCreator

### Description

This function is used for HTML-based report writing

### Usage

    reportCreator(indir = ".", outdir = .REPORT.DIR, db = NULL,
      prefix = NULL, varInfor = NULL)

### Arguments

`indir` | The directory of output files of function `parserGear`.
`outdir` | Output directory for this report
`db` | A FASTA format database file used for MS/MS searching. Usually, it is from the output of the function `dbCreator`.
`prefix` | It must be set the same with the parameter of "prefix" in function `parserGear`.
`varInfor` | It is a tab-delimited file contains detailed variation information and is from the output of the function `dbCreator`.

### Examples

    ## Step 1. Variation-associated database construction
    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")
    xref       <- system.file("extdata/sapFinder_test_BioMart.Xref.txt",
                            package="sapFinder")
    outdir     <- "db_dir"
    prefix     <- "sapFinder_test"
    db.files <- dbCreator(vcf=vcf, annotation=annotation,
                    refseq=refseq, outdir=outdir,
                    prefix=prefix,xref=xref)

    ## Step 2. MS/MS searching
    mgf.path   <- system.file("extdata/sapFinder_test.mgf",
                                package="sapFinder")
    fasta.path <- db.files[1]
    xml.path   <- runTandem(spectra=mgf.path, fasta=fasta.path, outdir=".",
                            tol=10, tolu="ppm", itol=0.1, itolu="Daltons")

    ## Step 3. Post-processing
    parserGear(file=xml.path, db=fasta.path, prefix=prefix,
                outdir="parser_outdir")

    ## Step 4. HTML-based report generation
    reportCreator(indir="parser_outdir", outdir="report", db=fasta.path,
                prefix=prefix, varInfor=db.files[2])

[Package sapFinder version 1.20.1 Index]