keep_DIU: Keep isoforms from genes with Differential Isoform Usage...

In ConesaLab/acorde: Isoform co-usage networks from single-cell RNA-seq data

Keep isoforms from genes with Differential Isoform Usage (DIU)

Description

Perform detection of genes with Differential Isoform Usage across clusters and remove isoforms from non-DIU genes.

Usage

keep_DIU(cluster_list, gene_tr_table)

Arguments

cluster_list	A list of character vectors, each containing the identifiers of the isoforms in a cluster.
gene_tr_table	A data.frame or tibble object containing two columns named transcript and gene, indicating gene-isoform correspondence.

Details

In single-cell RNA-Seq data, we consider Differential Isoform Usage (DIU) to occur when a gene shows changes in alternative isoform expression across cell types. For this to be possible, the first condition for a gene to be DIU is to first have at least two clustered isoforms. Accordingly, the function first removes all isoforms from genes that have a single isoform remaining in the clusters. To be positive for DIU, however, a gene must have at least two of its isoforms assigned to different clusters indicating that there is a change in isoform expression across cell types. Therefore, keep_DIU removes all isoforms that do not have at least one same-gene counterpart in another cluster, and that therefore do not belong to DIU genes.

Value

A list of character vectors, where each element corresponds to one cluster and contains the identifiers of the isoforms assigned to that cluster.

ConesaLab/acorde documentation built on Feb. 25, 2024, 4:16 a.m.