Filter genes based on expression

This function removes genes that are very lowly expressed.

Usage

fastSizeFactors_intl(Y)

filterGenes(spe, prop = 0.1)

# S4 method for SpatialExperiment
filterGenes(spe, prop = 0.1)

# S4 method for Seurat
filterGenes(spe, prop = 0.1)

Arguments

spe

a SpatialExperiment, Seurat, or SpatialFeatureExperiment object containing count data.

prop

a numeric, indicating the proportion of loci/cells where the gene should be expressed (default is 0.1, i.e., genes should be expressed in at least 10% of the loci/cells).

Value

a logical vector encoding which genes should be kept for further analysis.

Examples

data(HumanDLPFC)
keep <- filterGenes(HumanDLPFC)
table(keep)
#> keep
#> TRUE 
#> 5076