run_simple_stat {microbiomeMarker} | R Documentation |
Perform simple statistical analysis of metagenomic profiles. This function
is a wrapper of run_test_two_groups
and run_test_multiple_groups
.
run_simple_stat( ps, group, taxa_rank = "all", transform = c("identity", "log10", "log10p"), norm = "TSS", norm_para = list(), method = c("welch.test", "t.test", "white.test", "anova", "kruskal"), p_adjust = c("none", "fdr", "bonferroni", "holm", "hochberg", "hommel", "BH", "BY"), pvalue_cutoff = 0.05, diff_mean_cutoff = NULL, ratio_cutoff = NULL, eta_squared_cutoff = NULL, conf_level = 0.95, nperm = 1000, ... )
ps |
a |
group |
character, the variable to set the group |
taxa_rank |
character to specify taxonomic rank to perform
differential analysis on. Should be one of
|
transform |
character, the methods used to transform the microbial
abundance. See
|
norm |
the methods used to normalize the microbial abundance data. See
|
norm_para |
arguments passed to specific normalization methods |
method |
test method, options include: "welch.test", "t.test" and "white.test" for two groups comparison, "anova"and "kruskal" for multiple groups comparison. |
p_adjust |
method for multiple test correction, default |
pvalue_cutoff |
numeric, p value cutoff, default 0.05 |
diff_mean_cutoff, ratio_cutoff |
only used for two groups comparison,
cutoff of different means and ratios, default |
eta_squared_cutoff |
only used for multiple groups comparison, numeric,
cutoff of effect size (eta squared) default |
conf_level |
only used for two groups comparison, numeric, confidence level of interval. |
nperm |
integer, only used for two groups comparison, number of permutations for white non parametric t test estimation |
... |
only used for two groups comparison, extra arguments passed to
|
a microbiomeMarker
object.
run_test_two_groups()
,run_test_multiple_groups()
data(enterotypes_arumugam) ps <- phyloseq::subset_samples( enterotypes_arumugam, Enterotype %in% c("Enterotype 3", "Enterotype 2") ) run_simple_stat(ps, group = "Enterotype")