read.feat: Read a Feature File (GFF, BED, or GenePred)

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Read a features object from a file

Usage

read.feat(filename, pointer.only = FALSE)

Arguments

filename	the name of the file (can be GFF, BED, GenePred, or wig: rphast will auto-detect)
pointer.only	Whether to store object by reference instead of a data.frame

Details

The function will guess the format of the input file automatically.

Value

If pointer.only==FALSE, a data.frame with columns corresponding to the GFF specification. Otherwise, an object which is a pointer to an object stored in C.

Author(s)

Melissa J. Hubisz and Adam Siepel

See Also

feat for more description of features objects.

msa for more explanation of the pointer.only option.

http://www.sanger.ac.uk/resources/software/gff/spec.html for a detailed description of GFF file format. The columns in features objects mirror the GFF column definitions.

http://genome.ucsc.edu/FAQ/FAQformat for descriptions of BED and GenePred formats.

Examples

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "gencode.ENr334-100k.gff"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
dim(f)
f[1:10,]
unlink(featFile)

Example output

[1] 409   6
Features object
chr6	gencodeKnownGenes	AR	41405895	41405915	.	.	.	ENr334.1
chr6	gencodeKnownGenes	other	41405916	41406104	.	.	.	ENr334.2
chr6	gencodeKnownGenes	AR	41406105	41406608	.	.	.	ENr334.3
chr6	gencodeKnownGenes	other	41406609	41408719	.	.	.	ENr334.4
chr6	gencodeKnownGenes	AR	41408720	41408908	.	.	.	ENr334.5
chr6	gencodeKnownGenes	other	41408909	41411169	.	.	.	ENr334.6
chr6	gencodeKnownGenes	5'flank	41411170	41411370	.	.	.	ENr334.7
chr6	gencodeKnownGenes	5'UTR	41411371	41411592	.	.	.	ENr334.8
chr6	gencodeKnownGenes	CDS	41411593	41411644	.	.	.	ENr334.9
chr6	gencodeKnownGenes	intron	41411645	41411802	.	.	.	ENr334.10

rphast documentation built on May 1, 2019, 9:26 p.m.