collapseCellTypes: Collapse related cell types within a deconvolution result

In Nanostring-Biostats/SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Collapse related cell types within a deconvolution result

Description

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.

Usage

collapseCellTypes(fit, matching)

Arguments

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.

Value

A reshaped deconvolution result object

Examples

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
)

Nanostring-Biostats/SpatialDecon documentation built on Jan. 26, 2024, 8:20 p.m.