read.GTF: read gene annotation in GTF format

In qRNASeq: What the package does (short line)

Description

The function read GTF format annotation data into GRange objects by different features. The input GTF data can be downloaded from UCSC, Ensembl and so on. The function can split the regions into different features, such as exon, CDS, intron and utr.

Usage

read.GTF(file, feature = c("exon", "CDS", "intron", "utr"),
attributes = c("gene_id", "transcript_id", "gene_name",
"transcript_name", "protein_id")) 

Arguments

file	The gene annotation file in GTF format.
feature	A character vector that are used to classify the gene regions. It can be the combination of "exon", "CDS", "intron" and "utr".
attributes	The element names of the attribute column in the GTF data.

Details

More details about the GTF format can be found at: http://mblab.wustl.edu/GTF22.html

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.bed, 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.