rank_cells: Get the Rank of the Expression for each Gene in each Cell

In LieberInstitute/TREG: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Get the Rank of the Expression for each Gene in each Cell

Description

This function finds the rank of each gene's expression for each cell, grouped by the user defined variable. This data is used to compute the rank invariance value for each gene later with rank_invariance().

Usage

rank_cells(sce, group_col = "cellType", assay = "logcounts")

Arguments

sce	SummarizedExperiment-class object with the assay (defaults to logcounts).
group_col	name of the column in the colData() of sce that defines the group of interest.
assay	A character(1) specifying the name of the assay() in the sce object to use to rank expression values. Defaults to logcounts since it typically contains the normalized expression values.

Value

A named list() of matrix() objects. Each matrix() contains the rank values for the cells belonging to one group.

See Also

Other invariance functions: rank_group(), rank_invariance_express(), rank_invariance()

Examples

## Rank the genes for each cell, organized by "group" column
rank_cells(sce_zero_test, group_col = "group")

LieberInstitute/TREG documentation built on Dec. 15, 2024, 12:24 p.m.