runCollapseCellTypes {SpatialDecon}

R Documentation

Run collapseCellTypes

Description

Runs collapseCellTypes from an S4 object

Usage

runCollapseCellTypes(object, ...)

Arguments

object	An S4 object such as a GeoMxSet object
...	Arguments passed to collapseCellTypes

Value

A reshaped deconvolution result object

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)

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