is.ordered.msa: MSA is Ordered?

Description Usage Arguments Value Author(s) Examples

View source: R/msa.R

Description

Determines if an MSA object represents an ordered alignment.

Usage

1
2
## S3 method for class 'msa'
is.ordered(x)

Arguments

x

an MSA object

Value

a boolean indicating whether the columns are in order

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

1
2
3
4
5
6
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"))
is.ordered.msa(m)
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"), is.ordered=FALSE)
is.ordered.msa(m)

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