normalize,NanoStringGeoMxSet-method {GeomxTools} | R Documentation |
normalize GeoMxSet using different normalization methods
## 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, ... )
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 |
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)