Merge remote-tracking branch 'upstream/master'

RECETOX · Jul 25, 2024 · 33e290b · 33e290b
2 parents 5e04d51 + 0cde01b
commit 33e290b
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Showing 5 changed files with 1,945 additions and 1,869 deletions.
diff --git a/R/IsoFiltR.R b/R/IsoFiltR.R
@@ -42,8 +42,8 @@ filter_and_arrange_data <- function(peaks, sn) {
 #' A list containing two elements: "Carblist" and "Sulflist," each representing a list of data chunks.
 #' @export
 create_data_chunks <- function(data1) {
-  sect <- ceiling(nrow(data1)) / 10
-  over <- round(sect) * 0.15
+  sect <- ceiling(ceiling(nrow(data1))/10)
+  over <- ceiling(round(sect) * 0.15)
 
   data_chunks <- list()
   for (i in 1:10) {

diff --git a/R/MFAssign.R b/R/MFAssign.R
@@ -257,15 +257,19 @@ MFAssign <- function(peaks, isopeaks = "none", ionMode, lowMW=100,highMW=1000, P
 
     Test <-  dplyr::group_by(peaks, KMDTest, zstar)
     Test <- dplyr::mutate(Test, CH2_num = round(mass - min(mass))/14)
-    peaksend <- dplyr::filter(Test, CH2_num !=0 & CH2_num != (min(CH2_num[CH2_num!=min(CH2_num)])+1)&
-                                CH2_num != (min(CH2_num[CH2_num!=min(CH2_num)])+3))
 
-    names(peaksend)[1] <- "RA"
-    names(peaksend)[2] <- "Exp_mass"
-    peaksend <- peaksend[c(1,2)]
+     peaks1 <- dplyr::filter(Test, CH2_num == 0)
+     #peaks2 is just a dataframe to pull peaks3 and peaks4 from, not for additional usage
+     peaks2 <- dplyr::filter(Test, (CH2_num != 0 & CH2_num!=(min(CH2_num)+1)) == TRUE)
+     peaks3 <- dplyr::filter(peaks2, CH2_num == min(CH2_num))
+     peaks4 <- dplyr::filter(peaks2, (CH2_num==(min(CH2_num)+2)))
 
-    peaks <- dplyr::filter(Test, CH2_num ==0 | CH2_num == (min(CH2_num[CH2_num!=min(CH2_num)])+1) |
-                             CH2_num == (min(CH2_num[CH2_num!=min(CH2_num)])+3))
+    peaks <- rbind(peaks1, peaks3, peaks4)
+    rm(peaks1)
+    rm(peaks2)
+    rm(peaks3)
+    rm(peaks4)
+    rm(Test)
 
     peaks <- data.frame(RA = peaks[1], mass = peaks[2])
   }else{
@@ -279,17 +283,12 @@ MFAssign <- function(peaks, isopeaks = "none", ionMode, lowMW=100,highMW=1000, P
 
     Test <-  dplyr::group_by(peaks, KMDTest, zstar)
     Test <- dplyr::mutate(Test, CH2_num = round(mass - min(mass))/14)
-    peaksend <- dplyr::filter(Test, CH2_num !=0 & CH2_num != (min(CH2_num[CH2_num!=min(CH2_num)])+1)&
-                                CH2_num != (min(CH2_num[CH2_num!=min(CH2_num)])+3))
 
-    names(peaksend)[1] <- "RA_CH2"
-    names(peaksend)[2] <- "mass_CH2"
-    peaksend <- peaksend[c(1,2,5,6,7)]
     #
     peaks <- dplyr::filter(Test, RA > 0)
     #
     peaks <- data.frame(RA = peaks[1], mass = peaks[2])
-
+    rm(Test)
   }
   #################################
   Dummy <- data.frame(RA = c(-42,-42), mass = c(421.1147, 423.1293))