Calculates a panel of QC metrics from the junction count and PSI layers and
stores them directly in the embedded Seurat object's meta.data.
Existing columns with the same names are overwritten.
Usage
ComputeIsoformQC(object, ...)
# S4 method for class 'MatisseObject'
ComputeIsoformQC(object, min_coverage = 5L, verbose = TRUE)Value
The updated MatisseObject with QC columns added to
cell metadata.
The MatisseObject with QC columns added to
MatisseMeta(object) (i.e. the Seurat meta.data).
Details
Computed metrics:
- n_junctions_detected
Number of junctions with at least one read (junction mode only).
- total_junction_reads
Total junction read count across all junctions (junction mode only).
- n_events_covered
Number of splice events with PSI \(\geq\)
min_coverage(requires PSI to be calculated first).- pct_events_covered
Percentage of events with sufficient coverage.
- mean_psi
Mean PSI across covered events.