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Remove duplicated inputs and declare after parameter validation #11

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Remove duplicated inputs and declare after parameter validation #11

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8 changes: 5 additions & 3 deletions R/generateAnnotationThresholds.R
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Original file line number Diff line number Diff line change
Expand Up @@ -223,6 +223,8 @@ generateAnnotationThresholds <- function(gatingSet,
archDescriptionList=archDescriptionList
)

sampleNames <- flowWorkspace::sampleNames(gatingSet)
gatingSetPData <- flowWorkspace::pData(gatingSet)

#set up the faustData directory for check-pointing/metadata storage.
.initializeFaustDataDir(
Expand All @@ -238,8 +240,8 @@ generateAnnotationThresholds <- function(gatingSet,
#and their level in the imputation hierarchy.
.constructAnalysisMap(
projectPath = projectPath,
gspData = flowWorkspace::pData(gatingSet),
sampNames = flowWorkspace::sampleNames(gatingSet),
gspData = gatingSetPData,
sampNames = sampleNames,
experimentalUnit = experimentalUnit,
imputationHierarchy = imputationHierarchy,
debugFlag = debugFlag
Expand All @@ -258,7 +260,7 @@ generateAnnotationThresholds <- function(gatingSet,
#make sure the channel bounds conform to internal requirements
#test to see if there have been changes between faust runs.
.processChannelBounds(
samplesInExp = flowWorkspace::sampleNames(gatingSet),
samplesInExp = sampleNames,
projectPath = projectPath,
channelBounds = channelBounds,
debugFlag = debugFlag
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