setSeqQCFlags {GeomxTools} | R Documentation

## Add sequencing QC flags to NanoStringGeoMxSet object protocol data

### Description

Add sequencing QC flags to NanoStringGeoMxSet object protocol data

### Usage

    setSeqQCFlags(object, qcCutoffs = DEFAULTS)

### Arguments

`object` | name of the NanoStringGeoMxSet object to perform QC on
`qcCutoffs` | a list of qc cutoffs to use minSegmentReads, numeric to flag segments with less than this number of reads percentAligned, numeric to flag segments with less than this percent of aligned reads percentSaturation, numeric to flag segments with less than this percent of sequencing saturation

### 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"))
    setSeqQCFlags(demoData,
                     qcCutoffs=list(minSegmentReads=1000,
                                    percentAligned=80,
                                    percentSaturation=50))

[Package GeomxTools version 2.0.0 Index]