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)

[Package GeomxTools version 2.0.0 Index]