align-utils {Biostrings}R Documentation

Utility functions related to sequence alignment

Description

[TODO]

Usage

  consmat(x, freq=TRUE)

Arguments

x [TODO]
freq [TODO]

Details

consmat computes a consensus matrix for a set of equal-length strings assumed to be aligned.

See Also

BStringViews-class

Examples

  file <- system.file("Exfiles", "someORF.fsa", package="Biostrings")
  orf <- read.BStringViews(file, "fasta", "DNAString")

  ## To illustrate, the following example assumes the ORF data
  ## to be aligned for the first 10 positions (patently false):
  orf10 <- subviews(orf, 1, 10)
  consmat(orf10)

  ## For the character matrix containing the "exploded" representation
  ## of the views, do:
  as.matrix(orf10, mode="character")

[Package Biostrings version 2.6.6 Index]