collapseCellTypes {SpatialDecon} | R Documentation |
Given the input of an SpatialDecon result output and a list of which cell types to combine, returns a reshaped deconvolution result object with the specified cell types merged.
collapseCellTypes(fit, matching)
fit |
The object (a list) returned by the SpatialDecon algorithm |
matching |
A list object holding the mapping from beta's cell names to official cell names. See str(safeTME.matches) for an example. |
A reshaped deconvolution result object
data(mini_geomx_dataset) data(safeTME) data(safeTME.matches) # estimate background: mini_geomx_dataset$bg <- derive_GeoMx_background( norm = mini_geomx_dataset$normalized, probepool = rep(1, nrow(mini_geomx_dataset$normalized)), negnames = "NegProbe" ) # run basic decon: res0 <- spatialdecon( norm = mini_geomx_dataset$normalized, bg = mini_geomx_dataset$bg, X = safeTME ) res1 <- collapseCellTypes( fit = res0, matching = safeTME.matches )