M3DropGetMarkers {M3Drop} | R Documentation

## Identify marker genes

### Description

Calculates area under the ROC curve for each gene to predict the best group of cells from all other cells.

### Usage

      M3DropGetMarkers(expr_mat, labels)

### Arguments

`expr_mat` | a numeric matrix of normalized expression values, columns = samples, rows = genes.
`labels` | a vector of group ids for each cell/sample.

### Details

Uses the ROCR package to calculate the AUC for each gene for the group with the highest average rank. Significant is calculated using a Wilcox rank-sum test.

### Value

A dataframe with a row for each gene and columns: AUC, Group (which label this gene had the highest average rank for), and pval (uncorrected p-value of prediction).

### Examples

      library(M3DExampleData)
      norm <- M3DropConvertData(Mmus_example_list$data, is.counts=TRUE)
      marker_gene_table <- M3DropGetMarkers(norm, Mmus_example_list$labels)

[Package M3Drop version 1.12.0 Index]