setGeoMxQCFlags {GeomxTools} | R Documentation

## 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,
                     qcCutoffs=list(minNuclei=16000,
                                    minArea=20))

[Package GeomxTools version 2.0.0 Index]