View source: R/NanoStringGeoMxSet-qc.R
setBioProbeQCFlags | R Documentation |
Add probe QC flags to NanoStringGeoMxSet object feature data
setBioProbeQCFlags(object, qcCutoffs = DEFAULTS, removeLocalOutliers = TRUE)
object |
name of the NanoStringGeoMxSet object to perform QC on |
qcCutoffs |
a list of qc cutoffs to use
|
removeLocalOutliers |
boolean to determine if
local outliers should be excluded from |
NanoStringGeoMxSet
object with QCFlags
data frame
appended to protocolData
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)
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