ms1filename <- "15b.ms1"
peaklist <- read_ms1(ms1filename)
tol <- 0.005
justpeaks <- map(peaklist, 2)
justpeaks <- delete_unduplicated_peaklist(justpeaks, tol)
maxfeatures = 15000
t <- 1
toprint <- FALSE
while (t <= length(justpeaks)) {
numfeats <- 0
xs <- list()
ys <- list()
while (numfeats < maxfeatures) {
if (t >= length(justpeaks)) break()
cat("Numfeats", numfeats, "\n")
blockpeaks <- map(1:length(justpeaks[[t]]),
~c(justpeaks[[t]][[.x]][1], justpeaks[[t]][[.x]][2], t))
if (length(blockpeaks) == 0) {
t <- t + 1
next()
}
tol <- 0.01
clusts_cixes <- peaklist_to_cluster(blockpeaks, tol)
clusts <- clusts_cixes[[1]]
cixes <- clusts_cixes[[2]]
if (toprint) cat("num clusters:", length(clusts), length(clusts) / length(blockpeaks), "\n")
features <- list()
N <- length(clusts)
maxcharge <- 4
tol <- .01
if (toprint) cat("Hypothesizing isotope features \n")
for (n in seq_len(N)) {
p <- clusts[[n]]
n2 <- n + 1
for (c in maxcharge:1) {
isop <- PeakCluster(p$minmz + 1 / c, p$maxmz + 1 / c, 0, 0)
while (n2 < N) {
compare
}
}
}
}
}
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