PrepareAnnotationEnsembl: prepare annotation from ENSEMBL

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

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
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.
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
COSMIC	whether to download COSMIC data, default is FALSE.
...	additional arguments

Details

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

Value

several .RData file containing annotations needed for following analysis.

Author(s)

Xiaojing Wang

Examples

ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
host="sep2015.archive.ensembl.org", path="/biomart/martservice", 
archive=FALSE)

annotation_path <- tempdir()
transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888", 
    "ENST00000257430", "ENST00000508376", "ENST00000288602", 
    "ENST00000269571", "ENST00000256078", "ENST00000384871")

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

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.