getLineage {RCSL} | R Documentation

## 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)

[Package RCSL version 1.2.0 Index]