Correlation between nodes and leafs (deprecated) — corTreeMapping

Returns the correlation between expression of each cell and representative value for each node and leaf. NOTE: this function is unstable and will eventually be merged with corTreeMapping.

corTreeMapping_withFilter(
  dend = NA,
  refDat = NA,
  mapDat = refDat,
  medianExpr = NA,
  propExpr = NA,
  filterMatrix = NA,
  clusters = NA,
  numberOfGenes = 1200,
  outerLimitGenes = 7200,
  rankGeneFunction = function(x) getBetaScore(x, returnScore = FALSE),
  use = "p",
  ...
)

Arguments

dend: dendrogram for mapping. Ignored if medianDat is passed
refDat: normalized data of the REFERENCE data set. Ignored if medianExpr and propExpr are passed
mapDat: normalized data of the MAPPING data set. Default is to map the data onto itself.
medianExpr: representative value for each leaf. If not entered, it is calculated
propExpr: proportion of cells in each type expressing a given gene. If not entered, it is calculated
filterMatrix: a matrix of TRUE/FALSE values to indicate whether a given cluster is possible
clusters: cluster calls for each cell. Ignored if medianExpr and propExpr are passed
numberOfGenes: how many variables genes
outerLimitGenes: choose different numberOfGenes per cell from the top overall outerLimitGenes (to speed up function)
use, ...: additional parameters for cor
genesToMap: which genes to include in the correlation mapping

Value

a matrix of correlation values with rows as mapped cells and columns as clusters