matalign: Matrix Aligner

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Matrix Aligner

Description

Matrix Aligner is modified from Matalign-v4a. Matalign-v4a is a program to compare two positional specific matrices. The author of Matalign-v4a is Ting Wang and Gary Stormo.

Usage

matalign(
  pcms,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE,
  ...
)

Arguments

pcms	A list of pcm
method	Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
pseudo	pseudocount
revcomp	Check reverseComplement or not.
...	Not use.

Value

A data frame with alignment information. The column names are motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.

Examples

if(interactive() || Sys.getenv("USER")=="jianhongou"){
  fp <- system.file("extdata", package="motifStack")
  fs <- dir(fp, "pcm$")
  pcms <- importMatrix(file.path(fp, fs), format="pcm")
  matalign(pcms)
 }

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.