dbCreator {sapFinder} | R Documentation |
An integrated function to generate variation-associated database based on sample-specific NGS data or public SNV data.
dbCreator(vcf = NULL, annotation = NULL, refseq = NULL, outdir = "./", prefix = "test", xmx = NULL, xref = "noxref")
vcf |
Input VCF file name. This file contains the information of gene sequence variations. |
annotation |
Input annotation file name. It contains the gene annotation information and can be downloaded from UCSC Genome Browser.Currently it supports RefSeq genes and ENSEMBL genes annotation file. |
refseq |
Input mRNA sequences file with FASTA format. It can be downloaded from UCSC Genome Browser. |
outdir |
Output directory. |
prefix |
The prefix of output file. |
xmx |
The maximum Java heap size. The unit is "G". |
xref |
Optional external cross-reference file,generally it's downloaded through BioMart.If this file is provided,the final html report will present some relevant protein id or description. |
A vector containing two file names. One is a FASTA format file contains the mutated peptides, the normal protein sequences and their reverse versions, and the other is a tab-delimited file contains detailed variation information.
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)