align-utils {Biostrings} | R Documentation

## Utility functions related to sequence alignment

### Description

A variety of different functions used to deal with sequence alignments.

### Usage

      consmat(x, freq=TRUE)

### Arguments

`x` | A character vector, or an instance of either the BStringView, or the XStringAlign classes.
`freq` | If `TRUE` then letter frequencies (per position) are reported, otherwise counts.

### Details

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

### See Also

XStringViews-class, XStringAlign

### Examples

      file <- system.file("extdata", "someORF.fa", package="Biostrings")
      orf <- read.DNAStringSet(file, "fasta")

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

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

[Package Biostrings version 2.8.18 Index]