qcFlowObj: R6 object for Quality Control of flow data

In laderast/flowDashboard: Shiny Modules for Building interactive Dashboards for flow cytometry analysis

Description

R6 object for Quality Control of flow data

Usage

qcFlowObj

Format

qcFlowObj object.

Details

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

Value

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

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

See Also

QCOFromGatingSet

Examples

#Build a QCO Object from a GatingSet
gsFile <- system.file("extdata", "gvHDgs", package="flowDashboard")
gs <- load_gs(gsFile)
#default sampling is set to 4000 cells per FCS File
QCO <- QCOFromGatingSet(gs)
#look at slots of GatingObj
QCO

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

qc_data <- QCO$qcData
annot <- QCO$annotation
map_var <- QCO$mapVar
QCO <- qcFlowObj$new(qcData=qc_data, annotation=annot, mapVar = map_var)

laderast/flowDashboard documentation built on May 20, 2019, 7:33 p.m.