runReverseDecon {SpatialDecon}R Documentation

Run Reversedecon

Description

Runs reversedecon from an S4 object

Usage

runReverseDecon(object, ...)

Arguments

object

An S4 object such as a GeoMxSet object

...

Arguments passed to reversedecon

Value

list containing modeled gene expression's ~ cell scores

Examples

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)


[Package SpatialDecon version 1.4.3 Index]