runReverseDecon,NanoStringGeoMxSet-method {SpatialDecon}R Documentation

Run reversedecon on a NanostringGeomxSet object

Description

A wrapper for applying reversedecon to a NanostringGeomxSet object.

Usage

## S4 method for signature 'NanoStringGeoMxSet'
runReverseDecon(object, norm_elt = NULL, beta, epsilon = NULL)

Arguments

object

A NanostringGeomxSet object.

norm_elt

normalized data element in assayData.

beta

Matrix of cell abundance estimates, with cells in columns and observations in rows. Columns are aligned to "norm".

epsilon

All y and yhat values are thresholded up to this point when performing decon. Essentially says, "ignore variability in counts below this threshold."

Value

a valid GeoMx S4 object including the following items:

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]