Enr_by_q_cutoff: Enr_by_q_cutoff

In shihuang047/crossRanger: Cross-Application of Ranger Models using microbiome data

Enr_by_q_cutoff

Description

The significance of all features by q values.

Usage

Enr_by_q_cutoff(
  test_output,
  desc_stats_by_group_df,
  positive_class = NA,
  q_cutoff = 0.05
)

Arguments

test_output	The output from function mttest.
desc_stats_by_group_df	The output from function desc_stats_by_group.
positive_class	A string indicating the specified class in the factor y.
q_cutoff	A number indicating the cutoff of q values after fdr correction.

Examples

y <-factor(c(rep("A", 30), rep("B", 30)))
y1<-factor(c(rep("A", 15), rep("B", 15), rep("C", 15), rep("D", 15)))
x <- data.frame(rbind(t(rmultinom(7, 75, c(.201,.5,.02,.18,.099))),
            t(rmultinom(8, 75, c(.201,.4,.12,.18,.099))),
            t(rmultinom(15, 75, c(.011,.3,.22,.18,.289))),
            t(rmultinom(15, 75, c(.091,.2,.32,.18,.209))),
            t(rmultinom(15, 75, c(.001,.1,.42,.18,.299)))))
test_output<-mttest(x, y, p.adj.method="bonferroni", paired=FALSE)
test_output<-mttest(x, y1, p.adj.method="bonferroni", paired=FALSE)
desc_stats_by_group_df<-desc_stats_by_group(x, y, clr_transform=FALSE)
desc_stats_by_group_df<-desc_stats_by_group(x, y1, clr_transform=FALSE)
Enr_by_q_cutoff(test_output, desc_stats_by_group_df, q_cutoff=0.05, "A")

shihuang047/crossRanger documentation built on Feb. 7, 2023, 10:03 p.m.