percentile_expr: Summarize cell type-level expression using percentiles

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

Summarize cell type-level expression using percentiles

Description

For each of the isoforms in the single-cell data set, the function calculates percentile values using cell type-level expression values, providing an estimate of the expression distribution shown by a particular isoform in each of the cell types.

Usage

percentile_expr(data, id_table, percentile_no = 10, isoform_col = NULL)

Arguments

data	A data.frame or tibble object including isoforms as rows and cells as columns. Isoform IDs can be included as row names (data.frame) or as an additional column (tibble).
id_table	A data frame including two columns named cell and cell_type, in which correspondence between cell ID and cell type should be provided. The number of rows should be equal to the total number of cell columns in data, and the order of the cell column should match column (i.e. cell) order in data.
percentile_no	Integer indicating the number of percentiles to generate for each of the cell types. Should always be higher than 4 (quantiles) and lower than 100 (percentiles). Defaults to 10.
isoform_col	When a tibble is provided in data, a character value indicating the name of the column in which isoform IDs are specified.

Value

A tibble containing one column of percentile- summarized expression values per input transcript in data.

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