getExpData function

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

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.

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.

Returns

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)