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Filter cells based on the number of genes, counts, and mitochondrial reads.

filter_data.Rd

Deprecated: renamed to filter_cells() to read as "filter" (verb) + "cells" (object) rather than the vague "data", and to avoid leading with the bare word "filter", which collides conceptually with dplyr::filter()/stats::filter().

Usage

filter_data(
  x,
  num_mads = 3,
  min_genes = 500,
  max_genes = NULL,
  min_counts = NULL,
  max_counts = NULL,
  max_mt = 10,
  min_cells = 50,
  log_file = NULL
)

Arguments

x

A tibble with metadata (default method) or a Seurat object (Seurat method).

num_mads

Median absolute deviations for the outlier stage. NULL skips the stage.

min_genes

Minimum number of genes per cell. NULL for no cutoff.

max_genes

Maximum number of genes per cell. NULL for no cutoff.

min_counts

Minimum number of counts per cell. NULL for no cutoff.

max_counts

Maximum number of counts per cell. NULL for no cutoff.

max_mt

Maximum percentage of mitochondrial reads per cell. NULL for no cutoff.

min_cells

Minimum number of cells that must survive filtering. NULL skips the check.

log_file

Log file.

Value

Filtered data. See filter_cells().