runspatialdecon {SpatialDecon} | R Documentation |
Runs spatialdecon from an S4 object
runspatialdecon(object, ...)
object |
An S4 object such as a Seurat object or a GeoMxSet object |
... |
Arguments passed to spatialdecon |
decon results in list or in GeoMxSet object
##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")