plotNormFactorConcordance: Generate concordance figure of normalization factors based on...

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Generate concordance figure of normalization factors based on user provided factors

Description

For use with protein data ONLY.

Upper panels are the concordance plot. Lower panels are the standard deviation of the log2-ratios between the normalization factors

Usage

plotNormFactorConcordance(object, plotFactor, normfactors = NULL)

Arguments

object	name of the object class to subset NanoStringGeoMxSet, use the NanoStringGeoMxSet class
plotFactor	segment factor to color the plot by
normfactors	normalization factors from computeNormalizationFactors(). If NULL these are calculated automatically.

Examples

proteinData <- readRDS(file= system.file("extdata","DSP_Proteogenomics_Example_Data", 
"proteinData.rds", package = "GeomxTools"))

normConcord <- plotNormFactorConcordance(object = proteinData, plotFactor = "Segment_Type")
normConcord

Nanostring-Biostats/GeomxTools documentation built on April 14, 2024, 1:25 a.m.