getExpData: Function for extracting a filtered expression matrix from a...

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

Function for extracting a filtered expression matrix from a RaceID SCseq object

Description

This function for extracts a filtered expression matrix from a RaceID SCseq object. The filterdata function from the RaceID package has to be run on the SCseq object before.

Usage

getExpData(object, genes = NULL)

Arguments

object	RaceID SCseq object.
genes	Vector of valid gene identifiers corresponding to valid rownames of the input expression data. An expression matrix is returned only for these genes. Default is NULL and an expression matrix is returned for all genes retained after filtering of the SCseq object, i.e. all genes in genes slot of the SCseq object.

Value

noise Sparse Matrix with genes as rows and cells as columns after filtering.

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)

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