Description Usage Arguments Value Examples
View source: R/get_marker_genes.R
This is to identify marker genes for each cluster after SHARP clustering. It uses a method similar to that proposed in the SC3 package except two improvements: (1) it uses an adjusted threshold to select marker genes instead of using a hardthreshod (i.e., p-value < 0.01 and AUROC > 0.85), so that marker genes can be found for all clusters; (2) it uses a parallelization way to calculate the p-value and AUROC (areas under the curve of the Receiver Operating Characteristic) for each gene, thus much faster than SC3.
1 | get_marker_genes(scExp, y, theta, auc, pvalue, FC, ng, n.cores)
|
scExp |
the original expression matrix |
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. |
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.
1 2 | y = SHARP(scExp)
sginfo = get_marker_genes(scExp, y)
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