LRcell_gene_enriched_scores: Find most enriched cell types in bulk DE genes by Logistic...

In marvinquiet/LRcell: Differential cell type change analysis using Logistic/linear Regression

Find most enriched cell types in bulk DE genes by Logistic Regression

Description

This is a function which takes marker genes from single-cell RNA-seq as reference to calculate the enrichment of certain cell types in bulk DEG analysis. This algorithm borrows from Marques et al, 2016 (https://science.sciencemag.org/content/352/6291/1326.long).

Usage

LRcell_gene_enriched_scores(
  expr,
  annot,
  power = 1,
  parallel = TRUE,
  n.cores = 4
)

Arguments

expr	Expression matrix with rows as genes and columns as cells, can be an object of Matrix or dgCMatrix or a dataframe.
annot	Cell type annotation named vector with names as cell ids and values as cell types.
power	The penalty on fraction of cells expressing the genes.
parallel	Whether to run it in parallel.
n.cores	How many cores to use in parallel mode.

Value

A numeric matrix with rows as genes and columns as cell types, values are gene enrichment scores.

marvinquiet/LRcell documentation built on Sept. 16, 2022, 9:09 a.m.