AUCell_batch: Scores the SCE with AUCell

In MengyiShu/RASC: An implementation of RNA Analysis of Single Cell

Description

A function Scores a data matrix with AUCell in batches. Idea is to limit memory consumption when scoring with AUCell

Usage

AUCell_batch(inp_data, genesets, num_batches = 100)

Arguments

inp_data	SCE object
genesets	geneset that you want test with the SCE object,amed list of character vectors, each consisting of a set of gene symbols
num_batches	umber of batches to run AUCell for. More batches = fewer cells (observations)

Value

Returns an either an nxp matrix (samples x scores)

Examples

expr <- load_expression("mf_patient02.csv")
pathway_scores <- AUCell_batch(counts(expr), genesets = c(hallmarks), num_batches=20)
# Access pathway_scores
pathway_scores

MengyiShu/RASC documentation built on Dec. 17, 2021, 3:23 a.m.