normalize-NanoStringGeoMxSet-method: normalize

normalize,NanoStringGeoMxSet-methodR Documentation

normalize

Description

normalize GeoMxSet using different normalization methods

Usage

## S4 method for signature 'NanoStringGeoMxSet'
normalize(
  object,
  norm_method = c("quant", "neg", "hk", "subtractBackground"),
  fromElt = "exprs",
  toElt = "exprs_norm",
  housekeepers = HOUSEKEEPERS,
  ...
)

Arguments

object

name of the object class to perform normalization on

norm_method

the normalization method to be applied on the object

fromElt

name of the assayDataElement to normalize

toElt

name of the assayDataElement to store normalized values

housekeepers

optional vector of housekeeper target names

...

optional arguments

Value

a NanoStringGeoMxSet object with normalized counts and normalized factors

Examples

datadir <- system.file("extdata", "DSP_NGS_Example_Data",
  package = "GeomxTools"
)
demoData <- readRDS(file.path(datadir, "/demoData.rds"))
norm_object <- normalize(demoData[1:1000,1:10])

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.