View source: R/DAsimplestatistic.R
run_simple_stat  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")
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