get.mncs.win: MNCS for window size

In kathrinannaotte/haplovalidate: Detecting selected haplotype blocks in Evolve and Resequence experiments

MNCS for window size

Usage

under construction
get.mncs.win(cands, cmh, wins, wincut)

Arguments

cands
cmh
wins
wincut

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (cands, cmh, wins, wincut)
{
    snp.cmh <- merge(cands, cmh, by = c("chr", "pos"))
    scorewin <- c()
    for (k in wins) {
        snp.cmh[, `:=`(pos.bin, cut(pos, seq(0, max(pos), k *
            1e+06), include.lowest = T))]
        scorewin <- rbind(scorewin, (cbind(k, snp.cmh[, sum(as.numeric(score)),
            by = c("chr", "pos.bin")])))
    }
    scorewin <- data.table(scorewin)
    parameters <- c()
    for (c in unique(cands$chr)) {
        scorewin[chr == c, `:=`(score.sum, V1/sum(as.numeric(snp.cmh[chr ==
            c, score])))]
        cutoff <- scorewin[chr == c, median(score.sum), by = k]
        win <- cutoff[V1 >= wincut, k][1]
        parameters <- rbind(parameters, c(c, win))
    }
    colnames(parameters) <- c("chr", "win")
    parameters <- data.table(parameters)
    return(parameters)
  }

kathrinannaotte/haplovalidate documentation built on May 21, 2022, midnight