PrepareAnnotationGENCODE: prepare annotation from GENCODE

In proBAMr: Generating SAM file for PSMs in shotgun proteomics data

Description

prepare the annotation from GENCODE. Download GTF and FASTA files from GENCODE ftp first. Read introduction for more information.

Usage

PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path,
    dbsnp = NULL, splice_matrix = FALSE, COSMIC = FALSE, ...)

Arguments

gtfFile	specify GTF file location.
CDSfasta	path to the fasta file of coding sequence.
pepfasta	path to the fasta file of protein sequence.
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. "snp135")
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.
COSMIC	whether to download COSMIC data, default is FALSE.
...	additional arguments

Value

several .RData files containing annotations needed for further analysis.

Author(s)

Xiaojing Wang

Examples

gtfFile <- system.file("extdata", "test.gtf", package="proBAMr")
CDSfasta <- system.file("extdata", "coding_seq.fasta", package="proBAMr")
pepfasta <- system.file("extdata", "pro_seq.fasta", package="proBAMr")
annotation_path <- tempdir()
PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta,
                annotation_path, dbsnp=NULL,
                splice_matrix=FALSE, COSMIC=FALSE)

proBAMr documentation built on Nov. 8, 2020, 8:05 p.m.