summary.msa: MSA Summary

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

Description

Prints a short description of an MSA (multiple sequence alignment) object.

Usage

## S3 method for class 'msa'
summary(object, ..., print.seq = ncol.msa(object) < 100 &&
  nrow.msa(object) < 30, format = "FASTA", pretty.print = FALSE)

Arguments

object	an MSA object
...	additional arguments sent to print
print.seq	whether to supress printing of the alignment
format	to print sequence in if printing alignment
pretty.print	whether to pretty.print pretty-print sequence if printing alignment

Author(s)

Melissa J. Hubisz

See Also

print.msa

Examples

# read in an MSA stored in R
m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"))
summary(m)
#'
# read in an MSA stored by reference in C
m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"),
         pointer.only=TRUE)
summary(m)

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