matalign {motifStack} | R Documentation |
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.
matalign( pcms, method = c("Smith-Waterman", "Needleman-Wunsch"), pseudo = 1, revcomp = TRUE, ... )
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. |
A data frame with alignment information. The column names are motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.
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) }