runReverseDecon {SpatialDecon} | R Documentation |
Runs reversedecon from an S4 object
runReverseDecon(object, ...)
object |
An S4 object such as a GeoMxSet object |
... |
Arguments passed to reversedecon |
list containing modeled gene expression's ~ cell scores
library(GeomxTools) datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools") demoData <- readRDS(file.path(datadir, "/demoData.rds")) demoData <- shiftCountsOne(demoData) target_demoData <- aggregateCounts(demoData) target_demoData <- normalize(target_demoData, "quant") # run basic decon: res0 <- runspatialdecon(object = target_demoData, norm_elt = "exprs_norm", raw_elt = "exprs") # run reverse decon: target_demoData <- runReverseDecon(object = target_demoData, norm_elt = "exprs_norm", beta = pData(res0)$beta)