View source: R/BetweenGroup.test.R
BetweenGroup.test | R Documentation |
It runs standard univarate statistical tests (such as t.test, wilcox.test, oneway.test, kruskal.test) for all variates (columns) in the data.frame/data.matrix.
BetweenGroup.test( x, y, clr_transform = FALSE, p.adj.method = "bonferroni", positive_class = NA, q_cutoff = 0.2, paired = FALSE )
x |
A data.martrix or data.frame including multiple numeric vectors. |
y |
A factor with two or more levels. |
clr_transform |
A logical value indicates if clr transformation before statistical analysis of compositional microbiome data. |
p.adj.method |
A string indicating the p-value correction method. |
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. |
paired |
A logical indicating if paired between-group comparison is desired. |
...
Shi Huang
clr, t.test, wilcox.test, oneway.test, kruskal.test
x0 <- data.frame(t(rmultinom(16,160,c(.001,.5,.3,.3,.299))) + 0.65) 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))))) # clr_x<-compositions::clr(x) y<-factor(c(rep("A", 30), rep("B", 30))) y1<-factor(c(rep("A", 15), rep("B", 15), rep("C", 15), rep("D", 15))) system.time(BetweenGroup.test(x, y, clr_transform=FALSE)) system.time(BetweenGroup.test(x, y, clr_transform=TRUE)) system.time(BetweenGroup.test(x, y1, clr_transform=TRUE)) x_ <- data.frame(rbind(t(rmultinom(7, 7500, rep(c(.201,.5,.02,.18,.099), 100))), t(rmultinom(8, 7500, rep(c(.201,.4,.12,.18,.099), 100))), t(rmultinom(15, 7500, rep(c(.011,.3,.22,.18,.289), 100))), t(rmultinom(15, 7500, rep(c(.091,.2,.32,.18,.209), 100))), t(rmultinom(15, 7500, rep(c(.001,.1,.42,.18,.299), 100))))) y_<-factor(c(rep("A", 30), rep("B", 30))) y_1<-factor(c(rep("A", 15), rep("B", 15), rep("C", 15), rep("D", 15))) system.time(BetweenGroup.test(x_, y_)) system.time(BetweenGroup.test(x_, y_1))
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