Generate reference set of pseudo-cells

Creates a new reference set as input for cellToClusterMapping_byRank, where each 'cell' is the combiniation of several cells and this is run several times using different subsets of cells.

generateMultipleCellReferenceSet(
  refDat,
  clustersF,
  genesToUse = rownames(refDat),
  cellsPerMerge = 5,
  numberOfMerges = 10,
  mergeFunction = rowMedians,
  seed = 1
)

Arguments

refDat

normalized data of the REFERENCE data set

clustersF

factor indicating which cluster each cell type is actually assigned to in the reference data set

cellsPerMerge

Number of cells to include in each combo cell

numberOfMerges

Number of combo cells to include per cell type

mergeFunction

function for combining cells into combo cells (use rowMeans or rowMedians)

seed

for resproducibility

genesToMap

which genes to include in the correlation mapping

Value

list where first element is data matrix of multi-cells by genes and second element is a vector of corresponding clusters