LRcell_gene_enriched_scores {LRcell} | R Documentation |
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).
LRcell_gene_enriched_scores( expr, annot, power = 1, parallel = TRUE, n.cores = 4 )
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. |
A numeric matrix with rows as genes and columns as cell types, values are gene enrichment scores.