normalize,NanoStringGeoMxSet-method | R Documentation |
normalize GeoMxSet using different normalization methods
## S4 method for signature 'NanoStringGeoMxSet'
normalize(
object,
norm_method = c("quant", "neg", "hk", "subtractBackground"),
fromElt = "exprs",
toElt = "exprs_norm",
housekeepers = HOUSEKEEPERS,
...
)
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 |
a NanoStringGeoMxSet object with normalized counts and normalized factors
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])
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