cleanCounts: Filter a counts matrix

In JEFworks/MUDAN: Multi-sample Unified Discriminant ANalysis

Description

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

Usage

cleanCounts(counts, min.lib.size = 300, max.lib.size = 8000,
  min.reads = 1, min.detected = 1, verbose = 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: 300)
max.lib.size	Maximum number of genes detected in a cell. Cells with more genes will be removed (default: 8000)
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: TRUE)

Value

a filtered read count matrix

Examples

data(pbmcA)
dim(pbmcA)
mat <- cleanCounts(pbmcA)
dim(mat)

JEFworks/MUDAN documentation built on June 19, 2021, 6:46 a.m.