fastSizeFactors – SpaNorm

Filter genes based on expression

Description

This function computes the size factors using a fast but inaccurate approach. Size factors are computed using the direct estimate of library sizes (sum of all counts). Though fast, this approach does not cater for compositional biases in the data and therefore is less accurate than scran-based estimates.

Usage

fastSizeFactors(spe)

## S4 method for signature 'SpatialExperiment'
fastSizeFactors(spe)

Arguments

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

Value

a SpatialExperiment, Seurat, or SpatialFeatureExperiment, containing size factors in the ‘sizeFactor’ column of the column annotation.

Examples

library("SpaNorm")

data(HumanDLPFC)
HumanDLPFC <- fastSizeFactors(HumanDLPFC)
head(HumanDLPFC$sizeFactor)

AAACAAGTATCTCCCA-1 AAACACCAATAACTGC-1 AAACAGAGCGACTCCT-1 AAACAGCTTTCAGAAG-1 
         1.3854989          1.5920004          1.0583586          0.9358734 
AAACAGGGTCTATATT-1 AAACATTTCCCGGATT-1 
         1.7868073          1.0057331