run_ancombc  R Documentation 
Differential abundance analysis for microbial absolute abundance data. This
function is a wrapper of ANCOMBC::ancombc()
.
run_ancombc(
ps,
group,
confounders = character(0),
contrast = NULL,
taxa_rank = "all",
transform = c("identity", "log10", "log10p"),
norm = "none",
norm_para = list(),
p_adjust = c("none", "fdr", "bonferroni", "holm", "hochberg", "hommel", "BH", "BY"),
prv_cut = 0.1,
lib_cut = 0,
struc_zero = FALSE,
neg_lb = FALSE,
tol = 1e05,
max_iter = 100,
conserve = FALSE,
pvalue_cutoff = 0.05
)
ps 
a 
group 
the name of the group variable in metadata. Specifying

confounders 
character vector, the confounding variables to be adjusted.
default 
contrast 
this parameter only used for two groups comparison while there are multiple groups. For more please see the following details. 
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 
named 
p_adjust 
method to adjust pvalues by. Default is "holm".
Options include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY",
"fdr", "none". See 
prv_cut 
a numerical fraction between 0 and 1. Taxa with prevalences
less than 
lib_cut 
a numerical threshold for filtering samples based on library
sizes. Samples with library sizes less than 
struc_zero 
whether to detect structural zeros. Default is FALSE. 
neg_lb 
whether to classify a taxon as a structural zero in the corresponding study group using its asymptotic lower bound. Default is FALSE. 
tol 
the iteration convergence tolerance for the EM algorithm. Default is 1e05. 
max_iter 
the maximum number of iterations for the EM algorithm. Default is 100. 
conserve 
whether to use a conservative variance estimate of the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large. Default is FALSE. 
pvalue_cutoff 
level of significance. Default is 0.05. 
contrast
must be a two length character or NULL
(default). It is only
required to set manually for two groups comparison when there are multiple
groups. The order determines the direction of comparison, the first element
is used to specify the reference group (control). This means that, the first
element is the denominator for the fold change, and the second element is
used as baseline (numerator for fold change). Otherwise, users do required
to concern this parameter (set as default NULL
), and if there are
two groups, the first level of groups will set as the reference group; if
there are multiple groups, it will perform an ANOVAlike testing to find
markers which difference in any of the groups.
a microbiomeMarker
object.
Lin, Huang, and Shyamal Das Peddada. "Analysis of compositions of microbiomes with bias correction." Nature communications 11.1 (2020): 111.
ANCOMBC::ancombc
data(enterotypes_arumugam)
ps < phyloseq::subset_samples(
enterotypes_arumugam,
Enterotype %in% c("Enterotype 3", "Enterotype 2")
)
run_ancombc(ps, group = "Enterotype")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.