Nothing
################################################################################
getSegmentsPos <- function(chr, initialPos, finalPos, segments){
goodSegs <- which(
( as.numeric(gsub("chr","",segments[,1])) == as.numeric(gsub("chr","",chr)) |
gsub("chr","",segments[,1]) == gsub("chr","",chr) ) & (
(as.numeric(segments[,2]) >= (as.numeric(initialPos)) & as.numeric(segments[,2]) <= (as.numeric(finalPos)) ) |
(as.numeric(segments[,3]) >= (as.numeric(initialPos)) & as.numeric(segments[,3]) <= (as.numeric(finalPos)) ) |
(as.numeric(segments[,2]) <= (as.numeric(initialPos)) & as.numeric(segments[,3]) >= (as.numeric(finalPos)) )))
return(goodSegs)}
################################################################################
nr.modes <- function (y){
d1 <- diff(y)
signs <- diff(d1/abs(d1))
length(signs[signs == -2])}
################################################################################
findPeaks <- function (AF, bw) {
dens <- stats::density(AF, bw = bw, na.rm = T)
ydens <- dens$y
xdens <- dens$x
d1 <- diff(ydens)
signs <- diff(d1/abs(d1))
signs2 <- which(signs == -2)
if(length(signs2) > 0){
peaks <- data.frame(t(sapply(signs2, function(x, xdens, ydens){
list(xID=xdens[x], yID=ydens[x])}, xdens, ydens)))
} else {
cat(paste0("[",Sys.time() ,"] No peak found\n"))
peaks <- data.frame()
}
return(peaks)}
################################################################################
findMin <- function (AF, bw) {
dens <- stats::density(AF, bw = bw, na.rm=T)
ydens <- dens$y
xdens <- dens$x
d1 <- diff(ydens)
signs <- diff(d1/abs(d1))
signs2 <- which(signs == 2)
minima <- data.frame(t(sapply(signs2, function(x, xdens){xdens[x]}, xdens)))
return(minima)}
################################################################################
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