M3D_getmarkers: Identify marker genes

Description Usage Arguments Details Value Examples

Description

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

Usage

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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

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

M3Drop documentation built on Nov. 8, 2020, 5:06 p.m.