Filter cells by isoform QC thresholds

Removes cells that do not pass the specified thresholds on QC columns in MatisseMeta(object) (the Seurat meta.data). Run ComputeIsoformQC first to populate those columns.

Usage

FilterCells(object, ...)

# S4 method for class 'MatisseObject'
FilterCells(
  object,
  min_junctions = NULL,
  max_junctions = NULL,
  min_junction_reads = NULL,
  max_junction_reads = NULL,
  min_pct_covered = NULL,
  custom_filters = NULL,
  verbose = TRUE
)

Arguments

object

A MatisseObject.

...

Named numeric thresholds; see FilterCells.

min_junctions

Integer. Minimum n_junctions_detected. Default: NULL (no filter).

max_junctions

Integer. Maximum n_junctions_detected. Default: NULL.

min_junction_reads

Integer. Minimum total_junction_reads. Default: NULL.

max_junction_reads

Integer. Maximum total_junction_reads. Default: NULL.

min_pct_covered

Numeric (0–100). Minimum pct_events_covered. Default: NULL.

custom_filters

Named list of two-element numeric vectors c(min, max) applied to arbitrary metadata columns. Use NA for a one-sided bound. Default: NULL.

verbose

Logical. Default: TRUE.

Value

The filtered MatisseObject.

The filtered MatisseObject.

See also

ComputeIsoformQC