featureQC {airpart}R Documentation

Quality control on features

Description

Quality control on features

Usage

featureQC(sce, spike, detection_limit = 1, threshold = 0.25, sd = 0.03, pc = 2)

Arguments

sce

SingleCellExperiment with counts and ratio

spike

the character name of spike genes. The default is Ercc

detection_limit

Numeric scalar providing the value above which observations are deemed to be expressed.

threshold

A numeric scalar specifying the threshold above which percentage of cells expressed within each cell type. Default is 0.25

sd

A numeric scalar specifying the cell type weighted allelic ratio mean standard deviation threshold above which are interested features with highly variation. Default is 0.03

pc

pseudocount in the preprocess step

Value

A DataFrame of QC statistics includes

Examples


sce <- makeSimulatedData()
sce <- preprocess(sce)
featureQCmetric <- featureQC(sce)
keep_feature <- (featureQCmetric$filter_celltype &
  featureQCmetric$filter_sd &
  featureQCmetric$filter_spike)
sce <- sce[keep_feature, ]

# or manually setting threshold
featureQCmetric <- featureQC(sce,
  spike = "Ercc",
  threshold = 0.25, sd = 0.03, pc = 2
)
keep_feature <- (featureQCmetric$filter_celltype &
  featureQCmetric$sd > 0.02)

[Package airpart version 1.1.5 Index]