[BioC] what is the best way to get scores for matches from matchPWM() ?

[Lucas Carey]

Hi All,
I'm wondering what is the best way to get the score for every match
from matchPWM() in Biostrings

Right now, to score all matches to pwm in genome I do this:

#Find PWM hits for fwd & reverse complement of PWM for all chromosomes in genome
mmf <- sapply(1:Nchr,
function(chr){matchPWM(pwm,genome[[chr]],min.score=cutoff) }  )
mmr <- sapply(1:Nchr,
function(chr){matchPWM(reverseComplement(pwm),genome[[chr]],min.score=cutoff)
}  )
mmm <- c(mmf,mmr)

#Extract the sequences. RevComp where necessary.
Sequences <-  c( rapply(mmf,as.character,how='unlist'),
sapply(rapply(mmr,as.character,how='unlist'),function(x){c2s(rev(comp(s2c(x))))})
)

#convert to DNAStringSet for in order to score. This is quite slow
lcl_set  <- DNAStringSet(as.character(Sequences))
Scores  <- sapply(lcl_set,PWMscoreStartingAt,pwm=pwm)

This is incredibly inefficient. What is the best way to do this?

thanks

-Lucas