Merge pull request #91 from wverastegui/77_refactor_R_aplcms

Refactor find.turn.point.R and find.tol.time.R and recover.weaker.R

CHANGELOG.md

@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 - refactored `feature.align.R` [#63](https://github.com/RECETOX/recetox-aplcms/pull/63)[#88](https://github.com/RECETOX/recetox-aplcms/pull/88)
 - refactored `adjust.time.R` [#64](https://github.com/RECETOX/recetox-aplcms/pull/64)
+- refactored `find.tol.time.R` [#91](https://github.com/RECETOX/recetox-aplcms/pull/91)
+- refactored `find.turn.point.R` [#91](https://github.com/RECETOX/recetox-aplcms/pull/91)
 ### Removed
 
 ## [0.9.4] - 2022-05-10

DESCRIPTION

@@ -8,13 +8,13 @@ Authors@R: c(
 Description: This is a customized fork of the original work from Tianwei Yu.
         It takes the adaptive processing of LC/MS metabolomics data further
         with focus on high resolution MS for both LC and GC applications.
-Depends: R (>= 3.50), MASS, mzR, splines, doParallel, foreach, snow, dplyr, 
-        tidyr, stringr, tibble, tools, arrow
+Depends: R (>= 3.50), MASS, mzR, splines, doParallel, foreach,
+        snow, dplyr, tidyr, stringr, tibble, tools, arrow
 biocViews: Technology, MassSpectrometry
 License: GPL-2
 LazyLoad: yes
 NeedsCompilation: no
 Suggests: 
-    arrow, dataCompareR, testthat (>= 3.0.0)
+    dataCompareR, testthat (>= 3.0.0)
 Config/testthat/edition: 3
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1

NAMESPACE

@@ -8,25 +8,25 @@ export(bigauss.esti)
 export(bigauss.esti.EM)
 export(bigauss.mix)
 export(combine.seq.3)
-export(compute_all_times)
-export(compute_base_curve)
 export(compute_boundaries)
 export(compute_bounds)
 export(compute_breaks)
-export(compute_breaks_2)
+export(compute_delta_rt)
 export(compute_densities)
 export(compute_mass_density)
 export(compute_mass_values)
-export(compute_target_time)
+export(compute_target_times)
 export(cont.index)
 export(duplicate.row.remove)
+export(extract_features)
 export(extract_pattern_colnames)
 export(feature.align)
 export(find.tol)
 export(find.turn.point)
+export(find_local_maxima)
 export(get_custom_chr_tol)
 export(get_mzrange_bound_indices)
-export(get_raw_features_in_mzrange)
+export(get_rt_region_indices)
 export(get_times_to_use)
 export(hybrid)
 export(increment_counter)
@@ -35,9 +35,12 @@ export(load.lcms)
 export(load_data)
 export(load_file)
 export(make.known.table)
+export(mass.match)
+export(msExtrema)
 export(normix)
 export(normix.bic)
 export(plot_raw_profile_histogram)
+export(predict_mz_break_indices)
 export(prep.uv)
 export(proc.cdf)
 export(prof.to.features)

R/adaptive.bin.R

@@ -32,13 +32,6 @@ compute_breaks <- function(tol, masses, intensi, weighted) {
   return(breaks)
 }
 
-#' @export
-compute_boundaries <- function(mass.vlys, mass.pks, j){
-  mass.lower <- max(mass.vlys[mass.vlys < mass.pks[j]])
-  mass.upper <- min(mass.vlys[mass.vlys > mass.pks[j]])
-
-  return(list(lower = mass.lower, upper = mass.upper))
-}
 
 #' @export
 increment_counter <- function(pointers, that.n){
@@ -134,7 +127,7 @@ adaptive.bin <- function(x,
       for (j in 1:length(mass.pks))
       {
         # compute boundaries
-        boundaries <- compute_boundaries(mass.vlys, mass.pks, j)
+        boundaries <- compute_boundaries(mass.vlys, mass.pks[j])
 
         if (length(mass.pks) == 1){
           boundaries$lower <- boundaries$lower - 1
@@ -144,12 +137,7 @@ adaptive.bin <- function(x,
         that <- this_table |> dplyr::filter(mz > boundaries$lower & mz <= boundaries$upper)
 
         if (nrow(that) > 0) {
-          that <- combine.seq.3(that)
-
-          if (nrow(that) != 1) {
-            that <- that[order(that[, 1]), ]
-          }
-
+          that <- combine.seq.3(that) |> dplyr::arrange_at("mz")
           that.range <- diff(range(that$labels))
 
           if (that.range > 0.5 * time_range & length(that$labels) > that.range * min.pres & length(that$labels) / (that.range / aver.time.range) > min.pres) {