customProDB (version 1.12.0)

PrepareAnnotationEnsembl: prepare annotation from ENSEMBL

Description

prepare the annotation from ENSEMBL through biomaRt.

Usage

PrepareAnnotationEnsembl(mart, annotation_path, splice_matrix = FALSE, dbsnp = NULL, transcript_ids = NULL, COSMIC = FALSE, ...)

Arguments

mart

which version of ENSEMBL dataset to use. see useMart from package biomaRt for more detail.

annotation_path

specify a folder to store all the annotations

dbsnp

specify a snp dataset you want to use for the SNP annotation, default is NULL.

transcript_ids

optionally, only retrieve transcript annotation data for the specified set of transcript ids

splice_matrix

whether generate a known exon splice matrix from the annotation. this is not necessary if you don't want to analyse junction results, default is FALSE.

COSMIC

whether to download COSMIC data, default is FALSE.

...

additional arguments

Value

several .RData file containing annotations needed for following analysis.

Details

this function automaticlly prepares all annotation infromation needed in the following analysis.

Examples

ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
host="feb2012.archive.ensembl.org", path="/biomart/martservice",
archive=FALSE)

annotation_path <- tempdir()
transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888",
    "ENST00000257430", "ENST00000457016", "ENST00000288602",
    "ENST00000269571", "ENST00000256078", "ENST00000384871")

PrepareAnnotationEnsembl(mart=ensembl, annotation_path=annotation_path,
    splice_matrix=FALSE, dbsnp=NULL, transcript_ids=transcript_ids,
    COSMIC=FALSE)