comapre w pcm

compare two pcm objects

compareProfiles(
  pcm1,
  pcm2,
  method = c("Smith-Waterman", "Needleman-Wunsch"),
  pseudo = 1,
  revcomp = TRUE
)

Arguments

pcm1, pcm2

object of pcm
method

Alignment method. "Smith-Waterman" or "Needleman-Wunsch". Default is "Smith-Waterma"
pseudo

pseudocount
revcomp

Check reverseComplement or not.

Value

a list with names: motif1, motif2, alignmentScore, startPos1, startPos2, endPos1, endPos2, alignmentLength.