dbCreator {sapFinder} | R Documentation

## 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)

[Package sapFinder version 1.20.1 Index]