QCOFromGatingSet: Build a qcFlowObj from flowSet or gatingSet

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

Description

Build a qcFlowObj from flowSet or gatingSet

Usage

QCOFromGatingSet(gs, annotation = NULL, samplePop = 4000,
  qcMarkers = NULL, mapVar = NULL, objId = NULL)

Arguments

gs	- usually a GatingSet, but can also be a flowSet (useful for QC before gating)
annotation	- annotation. if NULL, will attempt to get from phenoData slot
samplePop	- number of points to sample from each flowFrame
qcMarkers	- list of markers to return that represent qcMarkers. Will return warning if the markers don't exist in data
mapVar	- maps the identifier in gs to annotation. If annotation is pulled from GatingSet phenoData, will be generated automatically
objId	- Unique object ID, used in ShinyModule to avoid namespace collisions. If NULL, will be generated automatically

Value

qcFlowObj

Examples

gsFile <- system.file("extdata", "gvHDgs", package="flowDashboard")
gs <- load_gs(gsFile)
#default sampling is set to 4000 cells per FCS File
QCO <- QCOFromGatingSet(gs)
QCO

#generate

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