expandClusters {SoupX}

Expands soup counts calculated at the cluster level to the cell level

Description

Given a clustering of cells and soup counts calculated for each of those clusters, determines a most likely allocation of soup counts at the cell level.

Usage

expandClusters(clustSoupCnts, cellObsCnts, clusters, cellWeights, verbose = 1)

Arguments

clustSoupCnts

Matrix of genes (rows) by clusters (columns) where counts are number of soup counts for that gene/cluster combination.

cellObsCnts

Matrix of genes (rows) by cells (columns) giving the observed counts

clusters

Mapping from cells to clusters.

cellWeights

Weighting to give to each cell when distributing counts. This would usually be set to the number of expected soup counts for each cell.

verbose

Integer giving level of verbosity. 0 = silence, 1 = Basic information, 2 = Very chatty, 3 = Debug.

Value

A matrix of genes (rows) by cells (columns) giving the number of soup counts estimated for each cell. Non-integer values possible.