align-utils {Biostrings} | R Documentation |
A variety of different functions used to deal with sequence alignments.
consmat(x, freq=TRUE)
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.
|
consmat
computes a consensus matrix for a set of equal-length strings
assumed to be aligned.
XStringViews-class, XStringAlign
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")