setSegmentQCFlags {GeomxTools} | R Documentation

## Add segment QC flags to protocol data

### Description

Add segment QC flags to protocol data

### Usage

    setSegmentQCFlags(object, qcCutoffs = DEFAULTS)

### Arguments

`object` | name of the object class to perform QC on NanoStringGeoMxSet, use the NanoStringGeoMxSet class
`qcCutoffs` | list of cutoffs and thresholds to use for QC

### 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"))
    setSegmentQCFlags(demoData,
                      qcCutoffs=list(minSegmentReads=1000,
                                     percentAligned=80,
                                     percentSaturation=50,
                                     minNegativeCount=10,
                                     maxNTCCount=60,
                                     minNuclei=16000,
                                     minArea=20))

[Package GeomxTools version 2.0.0 Index]