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junikimm717 3 years ago
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  1. 10
      specification.md
  2. 60
      src/script.def.R

10
specification.md

@ -24,6 +24,7 @@ isotopes.
- Independent of the ordering (it might get corrupted) - Independent of the ordering (it might get corrupted)
- Just search for chlorinated/brominated compounds. - Just search for chlorinated/brominated compounds.
- Use intensity + relative abundances that `isos` shows.
- usually, use_charges will be 1 - usually, use_charges will be 1
- Headers to use in script. - Headers to use in script.
@ -59,3 +60,12 @@ isotopes.
- Forseeable future, adapt to different isotopes. - Forseeable future, adapt to different isotopes.
- Capture multiple outputs of different isotopes. - Capture multiple outputs of different isotopes.
## Data Summary
- Flags for certainty of halogenated compounds
# Test Notes
- mztol seems to have a big impact on chlorine/bromine positives.

60
src/script.def.R

@ -1,27 +1,33 @@
library("nontarget") library("nontarget")
library("purrr") library("purrr")
#library("funprog")
library("enviPat") library("enviPat")
library("stringr") library("stringr")
library("parallel") library("parallel")
# Configurations ############################################################# # Configurations #############################################################
# file : decides which file to read in data from ############################# # file : decides which file to read in data from #############################
file <- "path/to/file"
file <- "/home/junikim/programming/patternmatch/data/allcluster_mz.csv"
#file <- "/home/junikim/programming/patternmatch/data/15_Clusters_for_Tuning_29June21.txt"
# check cluster 2846 # check cluster 2846
search_isos <- c("13C", "37Cl")
search_isos <- c("37Cl", "81Br")
# Minimum size of a cluster # Minimum size of a cluster
min_cluster_size <- 3
min_cluster_size <- 2
# Number of cores to be used (will be adjusted if not possible) # Number of cores to be used (will be adjusted if not possible)
use_cores <- 6 ##############################################################################
use_cores <- 6
# Do not edit below.
iso_length <- length(search_isos)
if (!("13C" %in% search_isos)) {
search_isos <- append(search_isos, "13C")
}
# Read in the Table ########################################################## # Read in the Table ##########################################################
table <- read.table(file, header=TRUE, sep="\t")
table <- read.table(file, header=TRUE, sep=",")
# Organize the tables by number ############################################## # Organize the tables by number ##############################################
fragments <- max(table[,"Spectra_Number"]) fragments <- max(table[,"Spectra_Number"])
@ -68,40 +74,56 @@ getdataframe <- function (fragment) {
mz <- getdata(fragment, "mz") mz <- getdata(fragment, "mz")
time <- getdata(fragment, "time") time <- getdata(fragment, "time")
Intensity <- getdata(fragment, "Intensity") Intensity <- getdata(fragment, "Intensity")
return(data.frame(mz=mz, time=time, Intensity=Intensity))
return(data.frame(mz=mz, Intensity=Intensity,time=time))
} }
# Incomplete: cannot get pattern.search function to work per cluster. #########
# Incomplete: Get the diagnostics for a cluster and turn them into a portable#
# format. (such as through tidyverse) ########################################
# initialize isotopes.
data(isotopes)
isos <- make.isos(isotopes,use_isotopes=search_isos, isos <- make.isos(isotopes,use_isotopes=search_isos,
use_charges=rep(1, length(search_isos))) use_charges=rep(1, length(search_isos)))
# returns both pattern.search result and fragment number.
diagnostics <- function(fragment) { diagnostics <- function(fragment) {
points <- getdataframe(fragment) points <- getdataframe(fragment)
ptrn <- pattern.search( ptrn <- pattern.search(
points, points,
isos, isos,
cutint=100000,
rttol=c(-0.2,0.2),
mztol=1000,
mzfrac=1.0,
cutint=1000,
rttol=c(-20,20),
# kept because of gc limitations.
mztol=3,
mzfrac=0.1,
ppm=TRUE, ppm=TRUE,
inttol=0.2,
inttol=0.05,
# Do not modify anything below. # Do not modify anything below.
rules=rep(FALSE, 11),
rules=rep(TRUE,11),
#rules=c(TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE),
deter=FALSE, deter=FALSE,
entry=50 entry=50
); );
return(ptrn)
return(c(ptrn, fragment))
} }
use <- Filter(function(x) usable[x], 1:fragments) use <- Filter(function(x) usable[x], 1:fragments)
results <- mclapply(use, diagnostics, mc.cores=use_cores) results <- mclapply(use, diagnostics, mc.cores=use_cores)
handle_res <- function(result) {
allzero <- function(v) {
for (x in v) {
if (x != 0)
return (FALSE)
}
return (TRUE)
}
v <- result$`Counts of isotopes`[seq(1,iso_length),"peak counts"]
if (!allzero(v)) {
print(result[[13]])
}
}
# Incomplete: Make the analysis more resiliant to different sorting.
for (result in results) {
handle_res(result)
}
############################################################################## ##############################################################################
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