prepareSpatialDecon: Preparing the inputs for SpatialDecon for doing deconvolution...

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Preparing the inputs for SpatialDecon for doing deconvolution on spatial data

Description

Preparing the inputs for SpatialDecon for doing deconvolution on spatial data

Usage

prepareSpatialDecon(
  spe,
  assay2use = "logcounts",
  negProbeName = "NegProbe-WTX",
  pool = NA
)

Arguments

spe	SpatialExperiment object.
assay2use	The name of the assay to use. By default is logcounts.
negProbeName	The name of the negative probe gene. By default is NegProbe-WTX.
pool	A vector indicates the pools of the genes. This is required when there are more than one Negative Probes.

Value

A list of two dataframes. The first data.frame is the normalised count, the second data.frame is the background for the data.

Examples

library(ExperimentHub)
eh <- ExperimentHub()

query(eh, "standR")
countFile <- eh[["EH7364"]]
sampleAnnoFile <- eh[["EH7365"]]

spe <- readGeoMx(countFile, sampleAnnoFile, rmNegProbe = FALSE)

out <- prepareSpatialDecon(spe)

DavisLaboratory/standR documentation built on Dec. 6, 2024, 9:55 p.m.