setBackgroundQCFlags {GeomxTools} | R Documentation

## Add background QC flags to NanoStringGeoMxSet object protocol data

### Description

Add background QC flags to NanoStringGeoMxSet object protocol data

### Usage

    setBackgroundQCFlags(object, qcCutoffs = DEFAULTS)

### Arguments

`object` | name of the NanoStringGeoMxSet object to perform QC on
`qcCutoffs` | a list of qc cutoffs to use minNegativeCount, numeric to flag segments with less than this number of counts maxNTCCount, numeric to flag segments with more than this number of NTC counts

### 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"))
    setBackgroundQCFlags(demoData,
                     qcCutoffs=list(minNegativeCount=10,
                                    maxNTCCount=60))

[Package GeomxTools version 2.0.0 Index]