extract.feature.msa: Extract features from an MSA object
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s) See Also

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

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

`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)

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

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!

Melissa J. Hubisz and Adam Siepel

sub.msa, [.msa

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