dbCreator {PGA} | R Documentation

## Create customized protein database from RNA-Seq data

### Description

The main function to create customized protein database from RNA-Seq data

### Usage

    dbCreator(gtfFile = NULL, vcfFile = NULL, bedFile = NULL,
      tabFile = NULL, annotation_path = NULL, outdir, outfile_name,
      lablersid = FALSE, COSMIC = FALSE, bool_get_longest = TRUE,
      organism = "Homo sapiens", make_decoy = TRUE, genome = NULL,
      debug = FALSE, ...)

### Arguments

`gtfFile` | A GTF format file containing novel transcripts information
`vcfFile` | A VCF format file containing SNV and INDEL information
`bedFile` | A BED format file from Tophat2 containing juction information.
`tabFile` | A Tab format file from Hisat2 containing juction information (e.g. splicesites.tab). As HISAT2 is a successor to both HISAT and TopHat2, we recommend that users switch to this option.
`annotation_path` | This directory contains numerous pieces of genome annotation information which can be downloaded by `PrepareAnnotationEnsembl2` or `PrepareAnnotationRefseq2`.
`outdir` | Output directory
`outfile_name` | Output file name
`lablersid` | A logical indicating whether to do the SNV annotation(dbSNP)
`COSMIC` | A logical indicating whether to do the SNV annotation(COSMIC)
`bool_get_longest` | When it's set as TRUE, the longest sequences will be retained after the DNA sequences are six-frame translated into protein sequences. Otherwise, the protein sequences more than 30 aa are retained.
`organism` | What is the Genus and species of this organism.Please use proper scientific nomenclature for example: "Homo sapiens" and not "human", default is "Homo sapiens".
`make_decoy` | A logical indicating whether to add the decoy sequences
`genome` | Genome information. This is a BSgenome object(e.g. Hsapiens). Default is NULL.
`debug` | Output the debug info (Default is <False>).
`...` | Additional arguments

### Value

The database file

### 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)
    dbCreator(gtfFile=gtffile,vcfFile=vcffile,bedFile=bedfile,
              annotation_path=annotation,outfile_name=outfile_name,
              genome=Hsapiens,outdir=outfile_path)

[Package PGA version 1.16.0 Index]