PGA (version 1.2.2)

dbCreator: 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, annotation_path = NULL, outdir, outfile_name, lablersid = FALSE, COSMIC = FALSE, bool_get_longest = TRUE, organism = "Homo sapiens", make_decoy = TRUE, genome = NULL, ...)

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 containing juction information

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.

...

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)