setBioProbeQCFlags {GeomxTools} | R Documentation

## Add probe QC flags to NanoStringGeoMxSet object feature data

### Description

Add probe QC flags to NanoStringGeoMxSet object feature data

### Usage

    setBioProbeQCFlags(object, qcCutoffs = DEFAULTS, removeLocalOutliers = TRUE)

### Arguments

`object` | name of the NanoStringGeoMxSet object to perform QC on
`qcCutoffs` | a list of qc cutoffs to use minProbeRatio, numeric between 0 and 1 to flag probes that have (geomean probe in all segments) / (geomean probes within target) less than or equal to this ratio percentFailGrubbs, numeric to flag probes that fail Grubb's test in greater than or equal this percent of segments
`removeLocalOutliers` | boolean to determine if local outliers should be excluded from `exprs` matrix

### 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"))
    demoData <- shiftCountsOne(demoData, elt="exprs", useDALogic=TRUE)
    setBioProbeQCFlags(demoData,
                       qcCutoffs=list(minProbeRatio=0.1,
                                      percentFailGrubbs=20),
                       removeLocalOutliers=TRUE)

[Package GeomxTools version 2.0.0 Index]