Merge pull request #52 from jasenfinch/devel

v0.10.1

Author: jasenfinch

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metaboWorkflows
 Title: Workflow Project Templates for Metabolomics Analyses
-Version: 0.10.0
+Version: 0.10.1
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Reproducible workflow project templates for metabolomics analyses using the `hrm` <https://jasenfinch.github.io/hrm/> R package ecosystem.
 URL: https://jasenfinch.github.io/metaboWorkflows/

NEWS.md

@@ -1,3 +1,9 @@
+# metaboWorkflows 0.10.1
+
+* Clarified the specification of argument `type` in the documentation of `target()`.
+
+* Added a suitable pre-treatment target expression for processing GC-MS profiling data.
+
 # metaboWorkflows 0.10.0
 
 * Workflow templates now include a `_targets.yaml` file for targets configuraion settings.

R/target.R

@@ -1,4 +1,4 @@
-#' S4 class to store target a definition
+#' S4 class to store a target definition
 #' @description An S4 class for storing a workflow target definition.
 #' @slot name the target name
 #' @slot command the R code to run the target as a string
@@ -294,7 +294,9 @@ setMethod('code',signature = 'Target',
 #' @param comment optional comment that precedes the target code
 #' @return An S4 object of class Target. 
 #' @details 
-#' Target types can be one of any provided by the `targets` or `tarchetypes` packages.
+#' The specified target `type` can be one of any provided by the `targets` package such as `tar_target`. 
+#' For target archetypes outside of `targets`, declare the package directly for argument 
+#' `type`. For instance, `type = "tarchetypes::tar_file"`. 
 #' @examples 
 #' workflow_target <- target('a_target',
 #'                           1 + 1,

R/targets.R

@@ -323,10 +323,27 @@ targetsSpectralProcessing <- function(x){
   return(processing_workflow)
 }
 
+preTreatmentRoutine <- function(x){
+  
+  pre_treat_modes <- 'metaboMisc::preTreatModes(results_spectral_processing,
+                                           parameters_pre_treatment)'
+  
+  pre_treat_GCMS <- 'metabolyseR::metabolyse(
+        profilePro::processedData(results_spectral_processing), 
+        profilePro::sampleInfo(results_spectral_processing),
+        parameters_pre_treatment)'
+  
+  switch(x,
+         `FIE-HRMS fingerprinting` = pre_treat_modes,
+         `NSI-HRMS fingerprinting` = pre_treat_modes,
+         `RP-LC-HRMS profiling` = pre_treat_modes,
+         `NP-LC-HRMS profiling` = pre_treat_modes,
+         `GC-MS profiling` = pre_treat_GCMS
+         )
+} 
+
 pre_treatment_commands <- list(
   parameters_pre_treatment = 'metaboMisc::detectPretreatmentParameters(results_spectral_processing)',
-  results_pre_treatment = 'metaboMisc::preTreatModes(results_spectral_processing,
-                                           parameters_pre_treatment)',
   export_pre_treatment = 'metaboMisc::exportData(results_pre_treatment,
                                                type = "pre-treated",
                                                outPath = "exports/pre-treated")',
@@ -359,7 +376,7 @@ targetsPretreatment <- function(x){
     ),
     results_pre_treatment = target(
       'results_pre_treatment',
-      !!parse_expr(pre_treatment_commands$results_pre_treatment),
+      !!parse_expr(preTreatmentRoutine(x)),
       comment = 'Perform data pre-treatment'
     ),
     export_pre_treatment_data = target(