Merge pull request #88 from VEuPathDB/computes-refactor

Computes refactor
VEuPathDB · Feb 28, 2024 · 2a8bf78 · 2a8bf78
2 parents d3c56d0 + 51a6a7e
commit 2a8bf78
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Showing 30 changed files with 71 additions and 1,090 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -49,16 +49,13 @@ Collate:
     'class-AbundanceData.R'
     'class-AbsoluteAbundanceData.R'
     'class-Comparator.R'
-    'class-ComputeResult.R'
-    'class-CorrelationResult.R'
     'method-alphaDiv.R'
     'method-betaDiv.R'
     'method-correlation.R'
     'method-differentialAbundance.R'
     'method-rankedAbundance.R'
     'methods-AbundanceData.R'
     'methods-Comparator.R'
-    'methods-ComputeResult.R'
     'methods-SampleMetadata.R'
     'methods-json.R'
     'microbiomeComputations-package.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,31 +3,21 @@
 export(AbsoluteAbundanceData)
 export(AbundanceData)
 export(Comparator)
-export(ComputeResult)
-export(CorrelationResult)
 export(DifferentialAbundanceResult)
 export(SampleMetadata)
 export(alphaDiv)
 export(betaDiv)
-export(correlation)
 export(differentialAbundance)
 export(getAbundances)
 export(getGroupLabels)
 export(getIdColumns)
 export(getSampleMetadata)
-export(predicateFactory)
 export(pruneFeatures)
 export(rankedAbundance)
 export(removeIncompleteSamples)
-export(selfCorrelation)
-export(writeData)
-export(writeMeta)
-export(writeStatistics)
 exportClasses(AbsoluteAbundanceData)
 exportClasses(AbundanceData)
 exportClasses(Comparator)
-exportClasses(ComputeResult)
-exportClasses(CorrelationResult)
 exportClasses(DifferentialAbundanceResult)
 exportClasses(SampleMetadata)
 exportMethods(alphaDiv)
@@ -38,24 +28,16 @@ exportMethods(getAbundances)
 exportMethods(getGroupLabels)
 exportMethods(getIdColumns)
 exportMethods(getSampleMetadata)
-exportMethods(predicateFactory)
 exportMethods(pruneFeatures)
 exportMethods(rankedAbundance)
 exportMethods(removeIncompleteSamples)
 exportMethods(selfCorrelation)
-exportMethods(writeData)
-exportMethods(writeMeta)
-exportMethods(writeStatistics)
 import(DESeq2)
 import(data.table)
 import(veupathUtils)
-importFrom(Hmisc,rcorr)
 importFrom(Maaslin2,Maaslin2)
 importFrom(Rcpp,sourceCpp)
 importFrom(S4Vectors,SimpleList)
-importFrom(SpiecEasi,pval.sparccboot)
-importFrom(SpiecEasi,sparcc)
-importFrom(SpiecEasi,sparccboot)
 importFrom(ape,pcoa)
 importFrom(methods,new)
 importFrom(methods,slot)

diff --git a/R/class-ComputeResult.R b/R/class-ComputeResult.R
diff --git a/R/class-CorrelationResult.R b/R/class-CorrelationResult.R
diff --git a/R/method-alphaDiv.R b/R/method-alphaDiv.R
@@ -86,7 +86,7 @@ setMethod("alphaDiv", signature("AbundanceData"), function(data, method = c('sha
       )
 
     result@computedVariableMetadata <- veupathUtils::VariableMetadataList(S4Vectors::SimpleList(computedVariableMetadata))
-    names(dt) <- stripEntityIdFromColumnHeader(names(dt))
+    names(dt) <- veupathUtils::stripEntityIdFromColumnHeader(names(dt))
     result@data <- dt 
 
     validObject(result)

diff --git a/R/method-betaDiv.R b/R/method-betaDiv.R
@@ -116,7 +116,7 @@ setMethod("betaDiv", signature("AbundanceData"), function(data, method = c('bray
     computedVariableMetadata <- veupathUtils::VariableMetadataList(lapply(displayNames, makeVariableMetadataObject))
 
     result@computedVariableMetadata <- computedVariableMetadata
-    names(dt) <- stripEntityIdFromColumnHeader(names(dt))
+    names(dt) <- veupathUtils::stripEntityIdFromColumnHeader(names(dt))
     result@data <- dt
 
     validObject(result)