bgc.informative: Return features indicating regions informative for bgc
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s)

Return features indicating regions informative for bgc

1	bgc.informative(align, foreground, tree, not.informative = FALSE)

`align`	An MSA object representing a multiple alignment
`foreground`	A character string giving the name of a branch (or a label given to several branches) indicating which branch should be in the foreground. The foreground branch is where GC-biased gene conversion is applied, and, if using a coding model, is where a test of positive selection can be performed.
`tree`	The phylogenetic tree to be used. Can be a newick string describing a tree, or an object of type `tm`.
`not.informative`	If TRUE, return the regions that are not informative for bgc.

An object of type feat indicating which regions are informative for bgc on the named foreground branch. If not.informative==TRUE, it will instead return the inverse of this, indicating which regions are not informative for bgc. The coordinates of the features object are in the frame of the reference species of the alignment.

Melissa J. Hubisz

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