View source: R/markerGenesAndMapping.r
rfTreeMapping | R Documentation |
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.
rfTreeMapping(
dend,
refDat,
clustersF,
mapDat = refDat,
p = 0.7,
low.th = 0.15,
seed = 1
)
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 |
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
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