subset.seqalignment: Get a subset of a seqalignment object, returning another...
In bomeara/sleq: sleq

Description Usage Arguments Details Value

Get a subset of a seqalignment object, returning another seqalignment object

## S3 method for class 'seqalignment'
subset(x, keep.site = NULL, kill.site = NULL,
  keep.taxon = NULL, kill.taxon = NULL, keep.gene = NULL,
  kill.gene = NULL, keep.pos = NULL, kill.pos = NULL, keep.type = NULL,
  kill.type = NULL)

`keep.site`	A vector of site positions to retain
`kill.site`	A vector of site positions to delete
`keep.taxon`	A vector of taxa (names or numbers) to retain
`kill.taxon`	A vector of taxa (names or numbers) to delete
`keep.gene`	A vector of genes to retain
`kill.gene`	A vector of genes to delete
`keep.pos`	A vector of codon positions to retain
`kill.pos`	A vector of codon positions to delete
`keep.type`	A vector of types to retain
`kill.type`	A vector of types to delete

This will only filter on those arguments passed in: if you give it a list of keep.sites, it will include all taxa, for example. You can filter on more than one feature at a time. The keep.* or kill.* arguments let you filter for objects to keep or remove.

A seqalignment object

bomeara/sleq documentation built on May 12, 2019, 11:36 p.m.