feat: Features Objects

Description

Create a new features object

Usage

feat(seqname="default", src=".", feature=".", start, end, score=NULL,
    strand=NULL, frame=NULL, attribute=NULL, pointer.only=FALSE)

Arguments

seqname

a character vector containing the name of the sequence

src

The source of the feature

feature

The feature type name

start

The start of the feature. Sequence numbering begins at 1.

end

The end of the feature. This is the last coordinate included in the feature.

score

The feature score, or NA if there is no score.

strand

A character string which is either "+", "-", or "." (if strand is not available or relevant).

frame

A 0, 1, or 2, which specifies whether the feature is in frame.

attribute

A feature attribute (character string).

pointer.only

Whether to store object as a pointer to an object in C, rather than as a data.frame in R.

Value

If pointer.only==FALSE, returns a data.frame whose format mirrors the GFF specification. Otherwise, returns a list with a single object, which is a external pointer to a C structure representing a features object.

Details

See http://www.sanger.ac.uk/resources/software/gff/spec.html for more detailed description of each parameter.

All arguments which are provided should be vectors of equal length.

If pointer.only==FALSE, the new object is a data frame, with columns mirroring the GFF Specification Otherwise, it is a list containing a single element, which is a pointer to an object stored in C.

Examples

Run this code

seq <- rep("hg18.chr6", 10)
src <- rep("fake_example", 10)
feature <- rep("CDS", 10)
start <- seq(1, 100, by=10)
end <- seq(10, 100, by=10)
f <- feat(seq, src, feature, start, end)
dim(f)
dim.feat(f)
f <- feat(seq, src, feature, start, end, pointer.only=TRUE)
dim.feat(f)