addPerROIQC: Add QC statistics to the Spatial Experiment object

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Add QC statistics to the Spatial Experiment object

Description

Add QC statistics to the Spatial Experiment object

Usage

addPerROIQC(
  spe_object,
  sample_fraction = 0.9,
  rm_genes = TRUE,
  min_count = 5,
  design = NULL
)

Arguments

spe_object	A SpatialExperiment object
sample_fraction	Double. Genes with low count in more than this threshold of the samples will be removed. Default is 0.9
rm_genes	Logical. Decide whether genes with low count in more than sample_fraction of the samples are removed from the dataset. Default is TRUE.
min_count	Integer. Minimum read count to calculate count threshold. Default is 5.
design	Generate using model.matrix, if this is specify, edgeR::filterByExpr will be used to filter genes.

Value

A SpatialExperiment object

Examples

data("dkd_spe_subset")
spe_filtered <- addPerROIQC(dkd_spe_subset)
spe_filtered

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.