isoform-methods

Reusable R functions for isoform-level single-cell RNA-seq, extracted from a long-read single-cell analysis. Each function takes plain vectors or a sparse matrix and returns a plain result, so the logic runs and tests without Seurat, IsoformSwitchAnalyzeR or any pipeline around it.

Functions

File	Provides
R/collapse_isoform_to_gene.R	collapse_isoform_to_gene(), strip_tx_version(). Sums fractional per-transcript counts to gene level. Counts are not rounded, because expectation-maximisation estimates are fractional by construction. Unmapped transcripts are returned in the stats rather than dropped.
R/isoform_switching.R	gene_totals(), isoform_fraction(), delta_if(), dominant_isoform(), delta_pi() and depth-envelope helpers. deltaPI follows the scisorseqr definition. Downsampling and bootstrap helpers are deterministic given a seed.
R/effect_sizes.R	cohens_d(), cliffs_delta(). Descriptive two-group effect sizes for per-cell scores.
R/qc_functions.R	Barcode-rank curves, pseudobulk aggregation and per-gene summaries.
R/cli.R	parse_cli(). A dependency-free argument parser for R drivers, where adding optparse to a pinned library is not an option.

Usage

source("R/isoform_switching.R")

if_a <- isoform_fraction(counts_a, gene)
if_b <- isoform_fraction(counts_b, gene)
dif  <- delta_if(if_a, if_b)

Tests

testthat::test_dir("tests/testthat")

85 tests on synthetic inputs, covering the aggregation arithmetic, isoform fraction and dIF definitions, deterministic tie-breaking in dominant-isoform selection, deltaPI against the scisorseqr definition, effect-size edge cases including zero variance and empty groups, and CLI type coercion. No data is included in this repository.

Requirements

R with Matrix. qc_functions.R additionally uses ggplot2, dplyr and scales. Tests need testthat.

References

Joglekar A, et al. (2021) for deltaPI. Squair JW, et al. (2021) and Murphy AE, Skene NG (2022) on pseudoreplication in single-cell differential expression, which is why the effect sizes here are reported without p-values.

Licence

MIT. See LICENSE.

Author

Philipp Graber. ORCID 0000-0002-3157-1434