Merge pull request #3 from jasenfinch/devel

v0.2.1

Author: jasenfinch

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: riches
 Title: Strucutral and Functional Enrichment Analyses
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",

NAMESPACE

@@ -35,8 +35,8 @@ importFrom(ggraph,theme_graph)
 importFrom(ggthemes,ptol_pal)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,set_names)
+importFrom(metabolyseR,analysisResults)
 importFrom(metabolyseR,explanatoryFeatures)
-importFrom(metabolyseR,modellingResults)
 importFrom(methods,new)
 importFrom(mzAnnotation,descriptors)
 importFrom(mzAnnotation,filterACCESSIONS)

R/enrichmentParameters.R

@@ -2,17 +2,17 @@
 #' @description Enrichment parameters.
 #' @param organism KEGG organism ID
 #' @param model model type to use for extracting explanatory features
-#' @param predictor predictor predictor name to use for extracting explanatory features
+#' @param response response variable name to use for extracting explanatory features
 #' @param threshold explanatory feature cutoff
 #' @importFrom methods new
 #' @export
 
-enrichmentParameters <- function(organism, model = 'randomForest', predictor = 'class', threshold = 0.05){
+enrichmentParameters <- function(organism, model = 'randomForest', response = 'class', threshold = 0.05){
   new('EnrichmentParameters',
       organism = organism,
       features = list(
         model = model,
-        predictor = predictor,
+        response = response,
         threshold = threshold
       ),
       structural = list()

R/functionalEnrichment.R

@@ -20,7 +20,7 @@
 #' @importFrom MFassign assignments
 #' @importFrom dplyr select distinct bind_rows
 #' @importFrom purrr map
-#' @importFrom metabolyseR modellingResults explanatoryFeatures
+#' @importFrom metabolyseR analysisResults explanatoryFeatures
 #' @importFrom magrittr set_names
 #' @export
 
@@ -59,9 +59,10 @@ setMethod('functionalEnrichment',signature = signature(analysis = 'Analysis',ass
               unique()
 
             explanFeat <- analysis %>%
-              modellingResults() %>%
-              {.[[parameters@features$model]][[parameters@features$predictor]]} %>%
-              explanatoryFeatures(threshold = parameters@features$threshold)
+              analysisResults('modelling') %>%
+              .[[parameters@features$model]] %>%
+              explanatoryFeatures(threshold = parameters@features$threshold) %>% 
+              filter(Response == parameters@features$response)
 
             comparisons <- explanFeat$Comparison %>%
               unique()

R/riches.R

@@ -1,2 +1,2 @@
 
-globalVariables(c('.','ACCESSION_ID','Name','Adduct','MF','Method','Pvalue','com','FELLA','label','Type'))
+globalVariables(c('.','ACCESSION_ID','Name','Adduct','MF','Method','Pvalue','com','FELLA','label','Type','Response'))