get_marker_genes_unlimited: Get marker genes of each cluster for huge-size single-cell...

In shibiaowan/SHARP: hyperfast and accurate single-cell RNA-Seq data clustering

Description

This is an version of finding marker genes for huge-size single-cell datasets (e.g., the size of the scRNA-seq data is so huge that the expression matrix can not be read into R; instead, a list of block-wise expression matrices is read into R.) This also corresponds to SHARP_unlimited(). Detailed specifications can be found in get_marker_genes().

Usage

get_marker_genes_unlimited(scExp, y, theta, auc, pvalue, n.cores)

Arguments

scExp	the list of original block-wise expression matrices
y	the clustering results after running SHARP.R
n.cores	number of cores to be used. The default is (n-1) cores, where n is the number of cores in your local computer or server.

Value

a matrix where each row represents each selected marker gene and each column represnts one property of the gene, including its cluster, p-value and AUROC.

Examples

y = SHARP(scExp)
sginfo = get_marker_genes_unlimited(scExp, y)

shibiaowan/SHARP documentation built on April 28, 2021, 1:56 p.m.