extract.feature.msa: Extract features from an MSA object

Description Usage Arguments Value Note Author(s) See Also

View source: R/msa.R

Description

Returns the subset of the MSA which appears in the features object.

Usage

1
extract.feature.msa(x, features, do4d = FALSE, pointer.only = FALSE)

Arguments

x

An object of type MSA

features

An object of type features denoting the regions of the alignment to extract.

do4d

If TRUE, then some elements of features must have type "CDS", and only fourfold-degenerate sites will be extracted.

pointer.only

If TRUE, return only a pointer to an object stored in C (useful for large alignments; advanced use only)

Value

An msa object containing only the regions of x appearing in the features object.

Note

If x was loaded with pointer.only==TRUE, then x will be modified to the return value of the function. Use extract.feature.msa(copy.msa(x), features,...) if you don't want this behavior!

Author(s)

Melissa J. Hubisz and Adam Siepel

See Also

sub.msa, [.msa


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