generateMultipleCellReferenceSet: Generate reference set of pseudo-cells

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

Generate reference set of pseudo-cells

Description

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.

Usage

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

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.