top_markers: Get top n markers from wilcoxauc

In immunogenomics/presto: Fast Functions for Differential Expression using Wilcox and AUC

Get top n markers from wilcoxauc

Description

Useful summary of the most distinguishing features in each group.

Usage

top_markers(
  res,
  n = 10,
  auc_min = 0,
  pval_max = 1,
  padj_max = 1,
  pct_in_min = 0,
  pct_out_max = 100
)

Arguments

res	table returned by wilcoxauc() function.
n	number of markers to find for each.
auc_min	filter features with auc < auc_min.
pval_max	filter features with pval > pval_max.
padj_max	filter features with padj > padj_max.
pct_in_min	Minimum percent (0-100) of observations with non-zero entries in group.
pct_out_max	Maximum percent (0-100) of observations with non-zero entries out of group.

Value

table with the top n markers for each cluster.

Examples

data(exprs)
data(y)

## first, run wilcoxauc
res <- wilcoxauc(exprs, y)

## top 10 markers for each group
## filter for nominally significant (p<0.05) and over-expressed (auc>0.5)
top_markers(res, 10, auc_min = 0.5, pval_max = 0.05)

immunogenomics/presto documentation built on March 26, 2024, 8:18 a.m.