read_annotation: Read a annotation file

In geneprophet/BSDMR: a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

Description

read_annotation reads a file containing annotation data, which will be used to select genomic regions for downstream analysis. The annotation file format is the following: "chromosome", "EnsemblID", "name","start", "end", "strand".

Usage

read_annotation(file)

Arguments

file	the path of annotation file

Value

A GRanges object. The GRanges object contains three additional metadata columns:

• id: EnsemblID

• center: the center of the region,(strat+end)/2

• annotation:the annotation of the region, it can be promoter,downstream,gene,UTR...

Author(s)

Hongen Kang [e-mail]

Examples

# Obtain the path to files
## Not run: 
#' file <- system.file("extdata", "human_chr22_annotation.txt", package = "BSDMR")
human_anno <- read_annotation(file)
file <- system.file("extdata", "mouse_chr15_annotation.txt", package = "BSDMR")
mouse_anno <- read_annotation(file)

## End(Not run)

geneprophet/BSDMR documentation built on March 3, 2021, 5:50 a.m.