runspatialdecon {SpatialDecon}

R Documentation

Run spatialdecon

Description

Runs spatialdecon from an S4 object

Usage

runspatialdecon(object, ...)

Arguments

object	An S4 object such as a Seurat object or a GeoMxSet object
...	Arguments passed to spatialdecon

Value

decon results in list or in GeoMxSet object

Examples

##Seurat
# get dataset
con <- gzcon(url("https://github.com/almaan/her2st/raw/master/data/ST-cnts/G1.tsv.gz"))
txt <- readLines(con)
temp <- read.table(textConnection(txt), sep = "\t", header = TRUE, row.names = 1)
# parse data
raw = t(as.matrix(temp))
norm = sweep(raw, 2, colSums(raw), "/") * mean(colSums(raw))
x = as.numeric(substr(rownames(temp), 1, unlist(gregexpr("x", rownames(temp))) - 1))
y = -as.numeric(substr(rownames(temp), 
                 unlist(gregexpr("x", rownames(temp))) + 1, nchar(rownames(temp))))
# put into a seurat object:
andersson_g1 = SeuratObject::CreateSeuratObject(counts = raw, assay="Spatial")
andersson_g1@meta.data$x = x
andersson_g1@meta.data$y = y

res <- runspatialdecon(andersson_g1)
str(res)

##GeomxTools
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")

demoData <- runspatialdecon(object = target_demoData, 
                            norm_elt = "exprs_norm",
                            raw_elt = "exprs")

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