runMergeTumorIntoX {SpatialDecon} | R Documentation |
Runs mergeTumorIntoX from an S4 object
runMergeTumorIntoX(object, ...)
object |
An S4 object such as a GeoMxSet object |
... |
Arguments passed to mergeTumorIntoX |
updated X matrix with new columns, "tumor.1", "tumor.2", ...
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") data(safeTME) tumor.ids <- as.logical(sample(x = c("TRUE","FALSE"), size = 88, replace = TRUE)) safeTME.with.tumor <- runMergeTumorIntoX(object = target_demoData, X = safeTME, K = 3, pure_tumor_ids = tumor.ids, norm_elt = "exprs_norm")