matalign: Matrix Aligner

Description Usage Arguments Value Examples

View source: R/matalign.R

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

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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

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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)
 }

motifStack documentation built on Nov. 8, 2020, 7:43 p.m.