ncol.msa: MSA Sequence Length.

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Returns the length of sequence in an MSA alignment.

Usage

## S3 method for class 'msa'
ncol(x, refseq = NULL)

Arguments

x	an MSA object
refseq	character vector giving name(s) of sequence whose length to return. The default NULL implies the frame of reference of the entire alignment.

Value

an integer vector containing the length of the named sequences. If refseq is NULL, returns the number of columns in the alignment.

Author(s)

Melissa J. Hubisz and Adam Siepel

See Also

msa

Examples

m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"))
ncol.msa(m)
ncol.msa(m, names.msa(m))

Example output

[1] 9
[1] 7 8 9

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