getLineage {RCSL} | R Documentation |
Infer the development lineage based on the clustering results from RCSL and the pseudotime
getLineage(drData, clustRes, pseudoTime, simMeasure = "kendall")
drData |
preprocessed gene expression data (each column represent a cell) |
clustRes |
the clustering results identified by RCSL |
pseudoTime |
inferred by PlotPseudoTime() using the similarity matrix S and starting cell |
simMeasure |
the calculation method of measuring the cluster centers' similarity |
lineage the cell lineages connected all the cluster centers based on the clustering results from RCSL
gfData <- GenesFilter(yan) TrueLabel <- ann$cell_type1 res_SimS <- SimS(gfData) C <- EstClusters(res_SimS$drData,res_SimS$S) res_BDSM <- BDSM(res_SimS$S,C) Pseudo <- PlotPseudoTime(res_SimS$S,TrueLabel,startPoint=1) getLineage(res_SimS$drData,res_BDSM$y,Pseudo$pseudoTime)