summary.compareDA: Summary differential analysis methods comparison results

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Summary differential analysis methods comparison results

Description

Summary differential analysis methods comparison results

Usage

## S3 method for class 'compareDA'
summary(
  object,
  sort = c("score", "auc", "fpr", "power"),
  boot = TRUE,
  boot_n = 1000L,
  prob = c(0.05, 0.95),
  ...
)

Arguments

object	an compareDA object, output from compare_DA().
sort	character string specifying sort method. Possibilities are "score" which is calculated as (auc - 0.5) * power - fdr, "auc" for area under the ROC curve, "fpr" for false positive rate, "power" for empirical power.
boot	logical, whether use bootstrap for confidence limites of the score, default TRUE. Recommended to be TRUE unless n_rep is larger then 100 in compare_DA().
boot_n	integer, number of bootstraps, default 1000L.
prob	two length numeric vector, confidence limits for score, default c(0.05, 0.95).
...	extra arguments affecting the summary produced.

Value

a data.frame containing measurements for differential analysis methods:

• call: differential analysis commands.

• auc: area under curve of ROC.

• fpr: false positive rate

• power: empirical power.

• fdr: false discover7y rate.

• score: score whch is calculated as (auc - 0.5) * power - fdr.

• ⁠score_*⁠: confidence limits of score.

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.