setBioProbeQCFlags: Add probe QC flags to NanoStringGeoMxSet object feature data

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

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[,1:10], 
                   qcCutoffs=list(minProbeRatio=0.1,
                                  percentFailGrubbs=20),
                   removeLocalOutliers=TRUE)

Nanostring-Biostats/GeomxTools documentation built on Dec. 17, 2024, 11:50 a.m.