make_test: Perform co-DIU statistical test for one gene pair
In ConesaLab/acorde: Isoform co-usage networks from single-cell RNA-seq data

make_test

R Documentation

Perform co-DIU statistical test for one gene pair

This function is called iteratively by test_codiu_genes to test cluster-dependent expression for a single pair of candidate co-DIU genes.

make_test(pair, data, cluster_list, gene_tr_table, cell_types)

`pair`	A character vector of length 2 indicating the gene IDs of a gene pair to test.
`data`	A data.frame or tibble including isoforms as rows and cells as columns. Isoform IDs can be included as row names (data.frame) or as an additional column (tibble).
`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 containing two columns named `transcript` and `gene`, indicating gene-isoform correspondence.
`cell_types`	A character vector including cell type assignments for the cell IDs in `data`.

Arguments are passed from test_codiu_genes.

A named list containing two elements, pvalue and test:

pvalue: A tibble containing two columns, cluster:cell_type and gene:cell_type, containing the p-value obtained in the likelihood ratio chi-square test (see test_codiu_genes) for each of these two interactions.
test: A tibble containing three columns, transcript, cluster and gene, each detailing the tested elements of the co-DIU interaction.