ncol.msa: MSA Sequence Length.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/msa.R

Description

Returns the length of sequence in an MSA alignment.

Usage

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## 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

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

rphast documentation built on May 30, 2017, 5:13 a.m.