getLineage: Infer the development lineage based on the clustering results...

In QinglinMei/RCSL: Rank Constrained Similarity Learning for single cell RNA sequencing data

Infer the development lineage based on the clustering results from RCSL and the pseudotime

Description

Infer the development lineage based on the clustering results from RCSL and the pseudotime

Usage

getLineage(drData, clustRes, pseudoTime, simMeasure = "kendall")

Arguments

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

Value

lineage the cell lineages connected all the cluster centers based on the clustering results from RCSL

Examples

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)

QinglinMei/RCSL documentation built on Feb. 16, 2024, 2:31 a.m.