Filter gene-set data.frame

Checks the objects gene-set data.frame for gene-sets that are composed of genes that exist in the given expression matrix.

adjustGeneSetDf(object, limit = 50)

Arguments

object

A valid spata-object.

limit

Numeric value between 1 and 100. The minimum percentage of gene-set genes that have to exist in the given expression matrix in order for a gene set to stay in the gene-set data.frame.

Value

An updated spata-object and an informative message about how many gene-sets have been discarded and how many gene-sets remain.

Details

E.g.: Gene-set 'x' is composed of 30 genes. The expression matrix however contains only 15 of them. If argument limit is set to 75 gene-set 'x' is removed since the percentage of genes of which the given expression matrix contains information about is only 50.