PrepareAnnotationRefseq: prepare annotation for Refseq

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

Description

prepare the annotation for Refseq through UCSC table browser.

Usage

PrepareAnnotationRefseq(genome = "hg19", CDSfasta, pepfasta, annotation_path,
  dbsnp = NULL, transcript_ids = NULL, splice_matrix = FALSE,
  ClinVar = FALSE, ...)

Arguments

genome	specify the UCSC DB identifier (e.g. "hg19")
CDSfasta	path to the fasta file of coding sequence.
pepfasta	path to the fasta file of protein sequence, check 'introduction' for more detail.
annotation_path	specify a folder to store all the annotations.
dbsnp	specify a snp dataset to be used for the SNP annotation, default is NULL. (e.g. "snp148")
transcript_ids	optionally, only retrieve transcript annotation data for the specified set of transcript ids. Default is NULL.
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.
ClinVar	whether to download ClinVar data, default is FALSE.
...	additional arguments

Value

several .RData file containing annotations needed for further analysis.

Author(s)

Xiaojing Wang

Examples

## Not run: 

transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499", "NM_004448",
        "NM_000179", "NR_029605", "NM_004333", "NM_001127511")
pepfasta <- system.file("extdata", "refseq_pro_seq.fasta", 
            package="customProDB")
CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta", 
            package="customProDB")
annotation_path <- tempdir()
PrepareAnnotationRefseq(genome='hg38', CDSfasta, pepfasta, annotation_path, 
            dbsnp=NULL, transcript_ids=transcript_ids, 
            splice_matrix=FALSE, ClinVar=FALSE)


## End(Not run)

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