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Calculate PSI matrix from junction counts

Source: R/generics.R, R/psi.R
CalculatePSI.Rd

Computes a Percent Spliced In (PSI) matrix for all splice events defined in event_data. Only applies to objects in junction mode; in event mode PSI is computed at construction time.

Usage

CalculatePSI(object, events = NULL, ...)

# S4 method for class 'MatisseObject'
CalculatePSI(
  object,
  events = NULL,
  min_coverage = 5L,
  na_fill = NA_real_,
  verbose = TRUE
)

# S4 method for class 'ANY'
CalculatePSI(
  object,
  events,
  min_coverage = 5L,
  na_fill = NA_real_,
  verbose = TRUE
)

Arguments

object

A MatisseObject in junction mode, or a sparse matrix (cells × junctions).

events

When object is a matrix: a data.frame with columns event_id, inclusion_junctions, and exclusion_junctions. When object is a MatisseObject this defaults to GetEventData(object).

...

Additional arguments passed to the method.

min_coverage

Integer. Minimum total reads per cell per event to report a PSI value. Default: 5.

na_fill

Numeric. Replacement for low-coverage entries. Default: NA_real_.

verbose

Logical. Print progress. Default: TRUE.

Value

A MatisseObject (when given one) or a PSI matrix.

  • MatisseObject: the input object with the "psi" assay populated inside the embedded Seurat object.

  • matrix: a dense matrix (cells × events) of PSI values.

Details

For each cell \(c\) and event \(e\):

$$PSI_{c,e} = \frac{\sum \text{inclusion reads}} {\sum \text{inclusion reads} + \sum \text{exclusion reads}}$$

Results are stored inside the embedded Seurat object as a Assay5 named "psi", with:

  • "data" layer: PSI values in \([0,1]\) (events × cells).

  • "counts" layer: inclusion read counts (events × cells).

  • "exclusion" layer: exclusion read counts (events × cells).

Entries where total coverage falls below min_coverage are set to NA in the "data" layer.

See also

ComputeIsoformQC, PlotHeatmap