sapFinder (version 1.10.0)

dbCreator: dbCreator

Description

An integrated function to generate variation-associated database based on sample-specific NGS data or public SNV data.

Usage

dbCreator(vcf = NULL, annotation = NULL, refseq = NULL, outdir = "./", prefix = "test", xmx = NULL, xref = "noxref")

Arguments

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.

Value

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.

Examples

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)