runMergeTumorIntoX,NanoStringGeoMxSet-method {SpatialDecon} | R Documentation |
A wrapper for applying mergeTumorIntoX to a NanostringGeomxSet object.
## S4 method for signature 'NanoStringGeoMxSet' runMergeTumorIntoX(object, X, K = 10, pure_tumor_ids = NULL, norm_elt = NULL)
object |
A NanostringGeomxSet object. |
X |
The training matrix |
K |
the number of clusters to fit |
pure_tumor_ids |
Vector identifying columns of norm that are pure tumor. Can be indices, logicals or column names. |
norm_elt |
norm data element in assayData |
an 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")