normalize,NanoStringGeoMxSet-method {GeomxTools}

R Documentation

normalize

Description

normalize GeoMxSet using different normalization methods

Usage

## S4 method for signature 'NanoStringGeoMxSet'
normalize(
  object,
  norm_method = c("quant", "neg", "hk", "subtractBackground"),
  data_type = c("RNA", "protein"),
  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
data_type	the data type of the object. Values maybe RNA, protein.
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)

---