dbCreator: Create customized protein database from RNA-Seq data

In Shawn-Xu/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

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)

Shawn-Xu/PGA documentation built on Aug. 28, 2020, 9:58 p.m.