PrepareAnnotationEnsembl2: Prepare annotation from ENSEMBL

In PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

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)

PGA documentation built on Nov. 8, 2020, 6:20 p.m.