R6 object for Quality Control of flow data

qcFlowObj

Format

qcFlowObj object.

Value

Object of R6Class with methods for getting/setting features for flowDashboard.

Details

This object is generated from QCOFromGatingSet. It is used in the following modules: qcModule and timeDriftModule.

Fields

qcData: data.table with three columns: idVar, variable, and value. Usually generated by QCOFromGatingSet.
annotation: Annotation (can be extracted as phenoData from a GatingSet) as data.table.
subsetOptions: set which columns in annotation to use for subsetting. Set by setSubsetAndSortOptions().
subsetOptionList: named list, where every entry corresponds to levels in a column in annotation.

Methods

new()
checkIntegrity(): This method checks whether the identifier used in annotation and data agree and ensures data integrity between the two.
setSubsetAndSortOptions(): set the subset and sortOptions
setMarkers(): set the markers in qcData and the markers to be displayed.
returnMergedData(): returns the merged qcData/annotation table as a data.table

Examples

#Build a QCO Object from a GatingSet
gsFile <- system.file("extdata", "gvHDgs", package="flowDashboard")
gs <- load_gs(gsFile)
#> Error in eval(expr, envir, enclos): could not find function "load_gs"
#default sampling is set to 4000 cells per FCS File
QCO <- QCOFromGatingSet(gs)
#> Error in match(x, table, nomatch = 0L): object 'gs' not found
#look at slots of GatingObj
QCO
#> Error in eval(expr, envir, enclos): object 'QCO' not found

#build QCO from using new()
#Unless you want to build from scratch components, we recommend using
#QCOFromGatingSet

qc_data <- QCO$qcData
#> Error in eval(expr, envir, enclos): object 'QCO' not found
annot <- QCO$annotation
#> Error in eval(expr, envir, enclos): object 'QCO' not found
map_var <- QCO$mapVar
#> Error in eval(expr, envir, enclos): object 'QCO' not found
QCO <- qcFlowObj$new(qcData=qc_data, annotation=annot, mapVar = map_var)
#> Error in .subset2(public_bind_env, "initialize")(...): object 'map_var' not found