Read a long-read transcript count matrix

Loads a per-cell transcript count matrix from a 10x-style MatrixMarket triplet (matrix.mtx, barcodes.tsv, features.tsv, optionally .gz) as produced by long-read / isoform quantifiers such as Bagpiper, FLAMES, or LIQA, and returns it in the transcripts x cells orientation with dimnames that CreateMatisseObject's transcript mode expects.

Usage

ReadTranscriptMatrix(
  mtx_dir,
  cells = NULL,
  strip_version = TRUE,
  orientation = c("auto", "cells_x_tx", "tx_x_cells"),
  verbose = TRUE
)

Arguments

mtx_dir

Directory holding matrix.mtx, barcodes.tsv and features.tsv (optionally .gz).

cells

Optional character vector of cell barcodes to keep (e.g. filtered barcodes). Barcodes absent from the matrix are dropped with a warning. Default: NULL (keep all).

strip_version

Logical. Strip a trailing .<digits> version suffix from transcript IDs; counts of IDs that collapse to the same stripped ID are summed. Default: TRUE.

orientation

One of "auto" (infer from dimensions; default), "cells_x_tx" (source is cells x transcripts; transpose), or "tx_x_cells" (source is already transcripts x cells).

verbose

Logical. Print progress. Default: TRUE.

Value

A dgCMatrix of transcript counts, transcripts x cells, transcript IDs as row names and barcodes as column names. Feed directly to CreateMatisseObject(transcript_counts = ...).

Details

Quantifiers disagree on matrix orientation (Bagpiper writes cells x transcripts; others write transcripts x cells), so orientation = "auto" infers it by matching the two matrix dimensions against the feature and barcode counts and transposes as needed.

Transcript-version landmine. SUPPA2 .ioe events and the quantifier may disagree on whether transcript IDs carry a version suffix (ENST...\.3). PSI aggregation (.build_indicator_matrix) matches IDs only after a _->- sanitisation; it never strips versions, so a mismatch silently zeroes PSI. strip_version = TRUE removes a trailing .<digits> from transcript IDs (summing counts of any IDs that collapse) to defend against this.

See also

ReadSTARsoloSJ for the short-read (junction) path; CreateMatisseObject.

Examples

if (FALSE) { # \dontrun{
txc <- ReadTranscriptMatrix("bagpiper/mats", cells = colnames(seu))
obj <- CreateMatisseObject(seu, transcript_counts = txc,
                           events = ioe_files)
} # }