Filter cells by QC thresholds

Removes cells that do not pass the specified thresholds on QC columns in MatisseMeta(object) (the Seurat meta.data). The columns nCount_isoform and nFeature_isoform are written at construction by CreateMatisseObject; nPercent_isoform is written by CalculatePSI.

Usage

FilterCells(
  object,
  min_features_isoform = NULL,
  max_features_isoform = NULL,
  min_counts_isoform = NULL,
  max_counts_isoform = NULL,
  min_pct_isoform = NULL,
  custom_filters = NULL,
  verbose = TRUE,
  ...
)

# S4 method for class 'MatisseObject'
FilterCells(
  object,
  min_features_isoform = NULL,
  max_features_isoform = NULL,
  min_counts_isoform = NULL,
  max_counts_isoform = NULL,
  min_pct_isoform = NULL,
  custom_filters = NULL,
  verbose = TRUE,
  ...
)

Arguments

object: A MatisseObject.
min_features_isoform: Integer. Minimum nFeature_isoform (number of junctions or transcripts with at least one read). Default: NULL.
max_features_isoform: Integer. Maximum nFeature_isoform. Default: NULL.
min_counts_isoform: Integer. Minimum nCount_isoform (total reads in the isoform assay). Default: NULL.
max_counts_isoform: Integer. Maximum nCount_isoform. Default: NULL.
min_pct_isoform: Numeric (0-100). Minimum nPercent_isoform (percentage of splice events with a non-NA PSI value). Requires CalculatePSI to have been run. 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.
...: Ignored; included for S4 generic compatibility.

Value

The filtered MatisseObject.

Usage

Arguments

Value

See also