.Random.seed
set.seed(currseed)
ms
cs
v
xs
realSeqs <- ms
realSeqsScores <- cs
simSeqs <- v
simSeqsScores <- xs
interval <- 0.01
    realSeqsTotalLength <- sum(lengths.ms(realSeqs))

    simSeqsTotalLength <- sum(lengths.ms(simSeqs))

    if (length(realSeqsScores$score) == 0L) return(data.frame())

       scores <- seq(from=max(realSeqsScores$score),to=min(realSeqsScores$score), by=-interval)

scores
    realCdf <- ecdf(-realSeqsScores$score)

    simCdf <- ecdf(-simSeqsScores$score)

    if (length(simSeqsScores$score) == 0L)
xs <- data.frame(score=scores, fdr=0)
dim(xs)
fdr <- data.frame(score=scores, fdr=0)
dim(fdr)
mm
ms <- seq
conservative <- TRUE
threshold <- -Inf
strand <- "best"
msPointer <- as.pointer.ms(ms)
mtemp <- mm
class(mm)
mtemp <- list(mtemp)
x <- .Call.rphast("rph_ms_score", msPointer$externalPtr, pwm, mtemp, length(mtemp)-1, conservative, threshold, strand)
x
q()
n
