cleanCounts: Filter a counts matrix

In JEFworks/MERingue: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Filter a counts matrix

Description

Filter a counts matrix based on gene (row) and cell (column) requirements.

Usage

cleanCounts(
  counts,
  min.lib.size = 1,
  max.lib.size = Inf,
  min.reads = 1,
  min.detected = 1,
  verbose = FALSE,
  plot = TRUE
)

Arguments

counts	A sparse read count matrix. The rows correspond to genes, columns correspond to individual cells
min.lib.size	Minimum number of genes detected in a cell. Cells with fewer genes will be removed (default: 1)
max.lib.size	Maximum number of genes detected in a cell. Cells with more genes will be removed (default: Inf)
min.reads	Minimum number of reads per gene. Genes with fewer reads will be removed (default: 1)
min.detected	Minimum number of cells a gene must be seen in. Genes not seen in a sufficient number of cells will be removed (default: 1)
verbose	Verbosity (default: FALSE)
plot	Whether to plot (default: TRUE)

Value

a filtered read count matrix

JEFworks/MERingue documentation built on June 11, 2022, 4:16 a.m.