dbCreator: dbCreator

In sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.

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)

sapFinder documentation built on Nov. 8, 2020, 5:59 p.m.