update to version 1.0.4

NEWS.md

 ![UltraMassExplorer](inst/figures/ume_package_icon.png)
 
+### Version 1.0.4
+- `assign_formulas()` adapted for formula libraries containing only one formula (e.g. when assigning the post-column standard in LCMS)
+- `calc_recalibrate_ms()` adapted for formula libraries containing only one formula (e.g. when assigning the post-column standard in LCMS)
+
+
 ### Version 1.0.3
 - New plot added for LCMS data (as provided by Dr. Xianyu Kong)
 - Post-column standard (Naproxen) added to ume::known_mf.

R/assign_formulas.R

@@ -53,7 +53,7 @@ assign_formulas <- function(pl, formula_library, msg = FALSE, ...){
     if(msg==T) message("  Peaklist mass range: ", round(pl[, min(m)],5), " - ", round(pl[, max(m)],5), " Da (", pl[, .N], " peaks)")
     if(msg==T) message("   Library mass range: ", round(formula_library[, min(mass)],5), " - ", round(formula_library[, max(mass)],5), " Da (", formula_library[, .N], " formulas)\n")
     a <- pl[, .N]
-    pl <- pl[m >= formula_library[, min(mass)] & m <= formula_library[, max(mass)],]
+    pl <- pl[m >= formula_library[, min(mass)]*0.9999 & m <= formula_library[, max(mass)]*1.0001,]
     warning("Mass range in peaklist is not completely covered by formula library.\n  "
             , a-pl[,.N], " peaks were truncated from the original peak list.\n")
   }

R/calc_neutral_mass.R

@@ -10,7 +10,7 @@
 #' @import data.table
 #' @export
 #' @return Adds columns 'm' for neutral molecular mass and m_min, m_max for the mass accuracy thresholds.
-#' @examples calc_neutral_mass(m = 199.32, pol = "neg")
+#' @examples calc_neutral_mass(mz = 199.32, pol = "neg")
 
 calc_neutral_mass <- function(mz, pol = c("neg", "pos", "neutral"), ...){
 

R/calc_recalibrate_ms.R

@@ -71,6 +71,15 @@ calc_recalibrate_ms <- function(pl,
 
   # browser()
 
+
+  # formula_library <- data.table(c = c(14, 28), h = c(14, 28), o = c(3, 6),
+  #                               n = c(0,0), s = c(0,0), p = c(0,0),
+  #                               `13c`=c(0,0), `15n`=c(0,0), `34s`=c(0,0),
+  #                               mass = c(233.11312455, 466.2262491), mf = c("C14H11D3O3", "C28H22D6O6"))
+
+  formula_library <- check_formula_library(formula_library)
+  # formula_library
+
   calibr_list <- match.arg(calibr_list)
   pol <- match.arg(pol)
 
@@ -108,7 +117,8 @@ calc_recalibrate_ms <- function(pl,
   mf_library[, vkey:=1:nrow(mf_library)]
 
   cal_peaks <- ume::assign_formulas(pl = pl[, ..cols], formula_library = mf_library, ...)
-
+  # cal_peaks <- assign_formulas(pl = pl[, ..cols], formula_library = mf_library, ma_dev = 2, pol = "neg")
+  # cal_peaks
 
   # maximum number of annotations per spectrum
   #cal_peaks[, .N, analysis_filename][,max(N)]
@@ -116,7 +126,7 @@ calc_recalibrate_ms <- function(pl,
   # Number of identified calibrant peaks in a spectrum
   check <-
     cal_peaks[, .(n_calibrants = .N), col_file_id][pl[, .(n_peaks = .N), col_file_id], on = col_file_id]
-  check
+
 
   # Check if there are files, for which less than 'min_no_calibrants' masses was found
   no_cal <- nrow(check[n_calibrants < min_no_calibrants | is.na(n_calibrants)])
@@ -298,7 +308,8 @@ calc_recalibrate_ms <- function(pl,
 
   # Recalibrate entire peaklist ####
   pl <- cal_stats[pl, on = col_file_id]
-  pl <- ume::calc_neutral_mass(pl, ...)
+  # pl[, pl:=calc_neutral_mass(...)]
+  pl[, m:=calc_neutral_mass(...)]
   pl[, m := (m - intercept) / slope]
 
   if (pol == "neg") {

_not_in_package/create_package.R

@@ -78,7 +78,7 @@
 
 # Local installation from tarball ####
   utils::install.packages(
-    "\\\\smb.isibhv.dmawi.de\\projects-noreplica\\p_ume\\UME\\ume_1.0.2.tar.gz",
+    "\\\\smb.isibhv.dmawi.de\\projects-noreplica\\p_ume\\UME\\ume_1.0.3.tar.gz",
     repos = NULL,
     type = "source"
   )
@@ -429,13 +429,14 @@ known_mf <-
 DBI::dbDisconnect(ch)
 
 known_mf[info1 %like% "Naprox"]
+is.data.table(known_mf)
 
 usethis::use_data(known_mf,
   overwrite = TRUE,
   version = 3,
   compress = "xz")
 
-# save(known_mf, file = "data/known_mf.rda", version = 3, compress = "xz")
+save(known_mf, file = "data/known_mf.rda", version = 2)
 
 known_mf <- ume::known_mf
 

man/calc_neutral_mass.Rd

@@ -22,6 +22,6 @@ The function also calculates the upper and lower mass boundaries for a mass accu
 Expects column names 'mz' for m/z values and 'i_magnitude' for mass peak magnitude.
 }
 \examples{
-calc_neutral_mass(m = 199.32, pol = "neg")
+calc_neutral_mass(mz = 199.32, pol = "neg")
 }
 \keyword{misc}