updateSC: Function for updating a RaceID SCseq object with VarID...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Function for updating a RaceID SCseq object with VarID results

Description

This function updates a RaceID SCseq object with a distance matrix or dimensionally reduced feature matrix, a clustering partition, and/or a matrix of gene expression variability, in order to utilize RaceID functions for visualization.

Usage

updateSC(object, res = NULL, cl = NULL, noise = NULL, flo = NULL)

Arguments

object	RaceID SCseq object.
res	List object returned by pruneKnn function to update SCseq with distance matrix and/or dimensionally reduced feature matrix in res. Default is NULL
cl	List object with clustering information, returned by the graphCluster function to update SCseq object with clustering partition and Fruchterman-Rheingold layout. Default is NULL.
noise	List object with the background noise model and a variability matrix, returned by the compNoise or compTBNoise function, to update SCseq object with a noise matrix. Default is NULL.
flo	Real number. Lower cutoff for the gene expression variability. All values < flo in the variability matrix are set to this level. Default is NULL and values are not reset.

Value

SCseq object with a distance matrix (slot distances) and a dimensionally reduced feature matrix (slot dimRed$x), or clustering partition (slot cpart and cluster$kpart) derived from the VarID analysis, and/or with a gene expression variability matrix in slot noise.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
d <- getExpData(sc)
res <- pruneKnn(d,distM=sc@distances,knn=10,alpha=1,no_cores=1,FSelect=FALSE)
cl <- graphCluster(res,pvalue=0.01)
sc <- updateSC(sc,res=res,cl=cl)
sc <- comptsne(sc)
plotmap(sc)

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.