import_bed {geneHapR}

import annotation files in BED format

Description

import bed files contains annotations into R as GRanges object

Usage

import_bed(con, quite = FALSE)

Arguments

con

A path, URL, connection or BEDFile object. For the functions ending in .bed, .bedGraph and .bed15, the file format is indicated by the function name. For the base export and import functions, the format must be indicated another way. If con is a path, URL or connection, either the file extension or the format argument needs to be one of “bed”, “bed15”, “bedGraph”, “bedpe”, “narrowPeak”, or “broadPeak”. Compressed files (“gz”, “bz2” and “xz”) are handled transparently.

quite

whether show message

Details

If there is no genome annotation file in GFF format for your interest species, a BED file is convenient to custom a simple annotation file for a gene. Here we suggest two type of BED format: BED6 and BED4.

As the definition of UCSC. The BED6 contains 6 columns, which are 1) chrom, 2) chromStart, 3) chromEnd, 4) name, 5) score and 6) strand. The BED4 format contains the first 4 column of BED6 format.

However, in gene haplotype statistics, we only care about the type of each site. Thus we use the fourth column to definition the transcripts name and "CDS" or "URTs", separated by a space, eg.:

Chr8 678 890 HD1.1 CDS . -

Chr8 891 989 HD1.1 five_prime_UTR . -

Chr8 668 759 HD1.2 CDS . -

Chr8 908 989 HD1.2 CDS . -

This example indicate a small gene named as HD1 have two transcripts, named as HD1.1 and HD1.2, separately. HD1 has a CDS and a UTR region; while HD1.2 has two CDS region.

Value

GRange object

Examples

bed.Path <- system.file("extdata", "annotation.bed6", package = "geneHapR")
bed <- import_bed(bed.Path)
bed