corTreeMapping_withFilter: Correlation between nodes and leafs (deprecated)

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

Correlation between nodes and leafs (deprecated)

Description

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.

Usage

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

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