setGeoMxQCFlags: Add GeoMx segment QC flags to NanoStringGeoMxSet object...

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol data

Description

Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol data

Usage

setGeoMxQCFlags(object, qcCutoffs = DEFAULTS)

Arguments

object	name of the NanoStringGeoMxSet object to perform QC on
qcCutoffs	a list of qc cutoffs to use minNuclei, numeric to flag segments with less than this number of nuclei minArea, numeric to flag segments with less than this um^2 area

Value

NanoStringGeoMxSet object with QCFlags data frame appended to protocolData

Examples

datadir <- system.file("extdata", "DSP_NGS_Example_Data",
                       package="GeomxTools")
demoData <- readRDS(file.path(datadir, "/demoData.rds"))
setGeoMxQCFlags(demoData[,1:10], 
                 qcCutoffs=list(minNuclei=16000, 
                                minArea=20))

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.