proBAMr (version 1.6.0)

PrepareAnnotationGENCODE: prepare annotation from GENCODE

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.

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)