read.GenePred: read gene annotation in GenePred format

In qRNASeq: What the package does (short line)

Description

The function read GenePred 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.GenePred(file, geneid = 12, feature = c("exon", "CDS", "intron",
"utr"), ...)

Arguments

file	The gene annotation file in GenePred format. The 9 additional fields are required.
geneid	If not NULL, it is the column number of the input file.
feature	A character vector that are used to classify the gene regions. It can be the combination of "exon", "CDS", "intron" and "utr".
...	More options for read.table to load the GenePred file.

Details

More details about the GenePred format can be found at: http://genome.ucsc.edu/FAQ/FAQformat#format9

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.bed

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.