rfTreeMapping: Tree-based mapping

View source: R/markerGenesAndMapping.r

rfTreeMappingR Documentation

Tree-based mapping

Description

Returns the mapping membership of each cell to each node and leaf using a tree-based method. This is a wrapper function for map_dend.

Usage

rfTreeMapping(
  dend,
  refDat,
  clustersF,
  mapDat = refDat,
  p = 0.7,
  low.th = 0.15,
  seed = 1
)

Arguments

dend

dendrogram for mapping

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

mapDat

normalized data of the MAPPING data set. Default is to map the data onto itself.

p

proportion of marker genes to include in each iteration of the mapping algorithm.

low.th

the minimum difference in Pearson correlation required to decide on which branch to map to. otherwise, a random branch is chosen.

seed

added for reproducibility

Value

a matrix of confidence scores (from 0 to 100) with rows as cells and columns as tree node/leafs. Values indicate the fraction of permutations in which the cell mapped to that node/leaf using the subset of cells/genes in map_dend


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