ecdf: ecdf plot for kst enrichment test

In zhuchcn/HTSet: High through-put experiment dataset container

Description

makes a ecdf plot for enrichment test result returned by enrichment_test with test equals to kst.

Usage

ecdf(x, ...)

## S3 method for class 'EnrichmentKST'
ecdf(
  x,
  level,
  alternative = c("greater", "less"),
  colors = c("blue", "red"),
  ...
)

Arguments

x	EnrichmentKST. Returned by enrichment_test when test equals to kst.
...	other arguments not supported
level	character. The level to plot the ecdf plot. Must be in the group.
alternative	character. Either greater or less
colors	character

Value

a ggplot2 object

Author(s)

Chenghao Zhu

See Also

enrichment_test

Examples

lpd = transform_by_sample(lipidome, function(x) log(x/sum(x)))
design = model.matrix(~Treatment * Timepoint + Subject, data = lpd$pdata)
fit = model_fit(lpd, design, "TreatmentMed:TimepointPre", "limma")
en = enrichment_test(lpd, fit, "class", "kst")
ecdf(en, level = "PC", alternative = "greater")

en = enrichment_test(lpd, fit, "class", "kst", alternative = "greater")
ecdf(en, level = "PC")

en = enrichment_test(lpd, fit, "class", "kst", alternative = "two.sided")
ecdf(en, level = "PC")

zhuchcn/HTSet documentation built on April 10, 2020, 4:51 p.m.