cellToClusterMapping_byRank: Cell-based cluster mapping

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

Cell-based cluster mapping

Description

Maps cells to clusters by correlating every mapped cell with every reference cell, ranking the cells by correlation, and the reporting the cluster with the lowest average rank.

Usage

cellToClusterMapping_byRank(
  mapDat,
  refDat,
  clustersF,
  genesToMap = rownames(mapDat),
  mergeFunction = rowMedians,
  useRank = TRUE,
  use = "p",
  method = "p"
)

Arguments

mapDat	normalized data of the MAPPING data set.
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
genesToMap	character vector of which genes to include in the correlation mapping
mergeFunction	function for combining ranks; the tested choices are rowMeans or rowMedians (default)
useRank	use the rank of the correlation (default) or the correlation itself to determine the top cluster
use	additional parameter for cor (use='p' as default)
method	additional parameter for cor (method='p' as default)

Value

a two column data matrix where the first column is the mapped cluster and the second column is a confidence call indicating how close to the top of the ranked list cells of the assigned cluster were located relative to their best possible location in the ranked list. This confidence score seems to be a bit more reliable than correlation at determining how likely a cell in a training set is to being correctly assigned to the training cluster.

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