gffToGRanges

path to a gff formatted file.
The file can end in <code>.gz</code>, <code>.bz2</code>, <code>.xz</code>, or <code>.zip</code>
and/or start with <code>http://</code> or <code>ftp://</code>. If the file is not compressed
it can also start with <code>https://</code> or <code>ftps://</code>.

gff.file

a character designating which elements to retain from the gff file (e.g. exon, CDS, ...)

filter

<code>boolean</code> whether the coordinates are 0 or 1 based. 0 is the default

zero.based

<code>boolean</code> if TRUE, add the chr prefix to seqlevels. FALSE by default

ensembl

Converts a gff formated data.frame into a GenomicRanges object.
The GenomicRanges object needs to be properly formated for the function to work.

A package for summary and annotation of genomic intervals. Users can visualize and 
	quantify genomic intervals over pre-defined functional regions, such as promoters, exons, 
	introns, etc. The genomic intervals represent regions with a defined chromosome position,
	which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, 
	methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal 
	information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

gffToGRanges: Converts a gff formated data.frame into a GenomicRanges object. The GenomicRanges object needs to be properly formated for the function to work.

Description

Usage

Arguments

Value

Examples