top_markers: Get top n markers from wilcoxauc

Description Usage Arguments Value Examples

View source: R/wilcoxauc.R

Description

Useful summary of the most distinguishing features in each group.

Usage

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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

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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 July 24, 2020, 11:47 p.m.