Nothing
unsafeFindInterval2 <- function (x, vec, rightmost.closed = FALSE, all.inside = FALSE)
{
nx <- as.integer(length(x))
nv <- as.integer(length(vec))
index <- integer(nx)
.C("find_interv_vec", xt = vec, n = nv, x = as.double(x),
nx = nx, as.logical(rightmost.closed), as.logical(all.inside),
index, DUP = FALSE, NAOK = TRUE, PACKAGE = "base")
index
}
unsafeFindInterval3 <- function (x, vec, rightmost.closed = FALSE, all.inside = FALSE) {
.Internal(findInterval(vec, x, rightmost.closed, all.inside))
}
PeakML.Methods.getRawMat <- function (allRawPeaks, scan_start,scan_finis, mz_start, mz_finis,correctedRT,uncorrectedRT)
{
scans <- scan_start:scan_finis
Rawpeaks <- allRawPeaks[scans]
rawRT <- uncorrectedRT[scans]
cRT <- correctedRT[scans]
peakExtract <- function (ind)
{
MZpeakset <- Rawpeaks[[ind]]
massData = MZpeakset[,1]
if ( version$major == '2' ) {
idxes = unsafeFindInterval2(c(mz_start, mz_finis), massData)
} else {
idxes = unsafeFindInterval3(c(mz_start, mz_finis), massData)
}
low = idxes[1] + (idxes[1] == 0 || mz_start != massData[idxes[1]])
high = idxes[2]
hit = low:high
if (high - low < 0) {
out <- NULL
} else {
dout <- MZpeakset[hit,]
dout <- rbind(dout,NULL)
maxIntens = which.max(dout[,2])
out <- c(rawRT[ind],cRT[ind],scans[ind],dout[maxIntens,1],dout[maxIntens,2])
}
out
}
RawMat <- do.call(rbind,lapply (1:length(Rawpeaks),peakExtract))
if (is.null(RawMat))
{
RawMat <- c(1,1,1,1,1)
}
RawMat <- rbind(RawMat,NULL)
if (!is.null(RawMat))
{
colnames (RawMat) <- c("rawRT","correctedRT","scan_id","mz","intensity")
}
RawMat
}
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