rank_invariance_express: Calculate the Rank Invariance of Each Gene from SCE object

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

Calculate the Rank Invariance of Each Gene from SCE object

Description

This function computes the Rank Invariance value for each gene, over the groups defined by the user. This function computes the same RI values as running rank_cells() + rank_group() + rank_invariance(). Genes with high RI values are considered good candidate TREGs. This function is more efficient than running the previous three functions.

Usage

rank_invariance_express(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 numeric() with the rank of invariance for each gene. High values represent low Rank Invariance, these genes are considered good candidate TREGs.

See Also

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

Examples

## Calculate RI for the sce object
## Highest RI value is best candidate TREG, and can change based on the grouping of interest
rank_invariance_express(sce_zero_test, group_col = "group")
rank_invariance_express(sce_zero_test, group_col = "cellType")

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