find_codiu_genes: Detect genes with co-Differential Isoform Usage
In ConesaLab/acorde: Isoform co-usage networks from single-cell RNA-seq data

find_codiu_genes

R Documentation

Detect genes with co-Differential Isoform Usage

Description

This function reports pairs of genes that present co-expressed isoforms given a list of previously-detected isoform clusters. The aim is to enable co-Differential Isoform Usage (co-DIU) analysis on the returned gene pairs, which will be candidates for co-DIU.

Usage

find_codiu_genes(cluster_list, gene_tr_table, parallel = TRUE, t = 4)

Arguments

`cluster_list`	A list of character vectors containing isoform IDs. Each element of the list represents a cluster of isoforms.
`gene_tr_table`	A data.frame or tibble object containing two columns named `transcript_id` and `gene_id`, indicating gene-isoform correspondence.
`parallel`	A logical. When `TRUE`, parallelization is enabled. The `future_map_lgl` function in the `furrr` is used.
`t`	An integer indicating the number of threads to be used for parallelization. This will be passed to the `plan` function from the `future` package via the `workers` argument.

Details

We define coordinated splicing patterns as a situation where post-transcriptional regulation, defined by isoform expression, can be detected independently of transcriptional regulation, i.e. gene-level expression. To detect splicing coordination, we defined co-Differential Isoform Usage (co-DIU) as a pattern where a group of genes shows co-expression of their isoforms, but no co-expression can be detected when only gene expression is considered. In the context of our pipeline, a set of potentially co-DIU genes will have at least two of their isoforms assigned to the same clusters, therefore showing detectable isoform-level co-expression, and suggesting coordinated splicing regulation in that group of genes (see Arzalluz-Luque et al. 2021).

Value

A matrix containing two rows and as many columns as potentially co-DIU gene pairs detected, that is, genes co-expressing isoforms across two or more clusters. Genes will be represented by the IDs provided in {gene_tr_table}.