read.bed: read gene annotation in bed format

In qRNASeq: What the package does (short line)

Description

The function read bed format annotation data into GRange objects by different features. It can split the regions into different features, such as exon, CDS, intron and utr.

Usage

read.bed(file, feature = c("exon", "CDS", "intron", "utr"))

Arguments

file	The gene annotation file in bed format. The 9 additional fields are required.
feature	A character vector that are used to classify the gene regions. It can be the combination of "exon", "CDS", "intron" and "utr".

Details

More details about the BED format can be found at: http://genome.ucsc.edu/FAQ/FAQformat#format1

Value

The results return a list of GRanges object according to the specified features. By default, the features "exon", "CDS", "intron", "utr" are specified. The results will contain a list of regions that contains exon, coding sites, intron, 3 end UTR and 5 end UTR from the input GTF file.

Author(s)

Qiang Hu

See Also

read.GTF, read.GenePred

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

qRNASeq documentation built on May 2, 2019, 4:26 p.m.