PrepareAnnotationEnsembl {customProDB} | R Documentation |
prepare the annotation from ENSEMBL through biomaRt.
PrepareAnnotationEnsembl(mart, annotation_path, splice_matrix = FALSE, dbsnp = NULL, transcript_ids = NULL, COSMIC = FALSE, ...)
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 |
this function automaticlly prepares all annotation infromation needed in the following analysis.
several .RData file containing annotations needed for following analysis.
Xiaojing Wang
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)