dbCreator {PGA} | R Documentation |
The main function to create customized protein database from RNA-Seq data
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, ...)
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
|
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 |
The database file
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)