PGA (version 1.2.2)

PrepareAnnotationEnsembl2: Prepare annotation from ENSEMBL

Description

Prepare the annotation from ENSEMBL through biomaRt. This function is modified from the function PrepareAnnotationEnsembl in customProDB.

Usage

PrepareAnnotationEnsembl2(mart, annotation_path, splice_matrix = FALSE, dbsnp = NULL, transcript_ids = NULL, COSMIC = FALSE, ...)

Arguments

mart

See detail in function PrepareAnnotationEnsembl.

annotation_path

See detail in function PrepareAnnotationEnsembl.

splice_matrix

See detail in function PrepareAnnotationEnsembl.

dbsnp

See detail in function PrepareAnnotationEnsembl.

transcript_ids

See detail in function PrepareAnnotationEnsembl.

COSMIC

See detail in function PrepareAnnotationEnsembl.

...

Additional arguments

Value

Several .RData file containing annotations needed for following analysis.

See Also

PrepareAnnotationRefseq2.

Examples

ensembl <- biomaRt::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")

PrepareAnnotationEnsembl2(mart=ensembl, annotation_path=annotation_path,
                          splice_matrix=FALSE, dbsnp=NULL, transcript_ids=transcript_ids,
                          COSMIC=FALSE)