computeNormalizationFactors: Generate normalization factors

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Generate normalization factors

Description

For use with protein data ONLY.

Generate normalization factors for protein data to determine the best normalization method

Usage

computeNormalizationFactors(
  object,
  igg.names = NULL,
  hk.names = NULL,
  area = NULL,
  nuclei = NULL
)

Arguments

object	name of the object class to subset NanoStringGeoMxSet, use the NanoStringGeoMxSet class
igg.names	names of IgGs, if NULL IgGs will be detected automatically
hk.names	names of HK, if NULL HK will be detected automatically
area	name of area column in annotation sheet, optional
nuclei	name of nuclei column in annotation sheet, optional

Examples

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

normfactors <- computeNormalizationFactors(object = proteinData)

normfactors_withAreaNuclei <- computeNormalizationFactors(object = proteinData,
area = "AOI.Size.um2", nuclei = "Nuclei.Counts")

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