Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 |
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.
1 2 3 4 5 6 | 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)
}
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