PrepareAnnotationEnsembl2 {PGA} | R Documentation

## 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="grch37.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)

[Package PGA version 1.20.0 Index]