setSeqQCFlags: Add sequencing QC flags to NanoStringGeoMxSet object protocol...

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

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[,1:10], 
                 qcCutoffs=list(minSegmentReads=1000, 
                                percentAligned=80, 
                                percentSaturation=50))

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