run_lefse {microbiomeMarker} | R Documentation |
Perform Metagenomic LEFSe analysis based on phyloseq object.
run_lefse( ps, group, subgroup = NULL, taxa_rank = "all", transform = c("identity", "log10", "log10p"), norm = "CPM", norm_para = list(), kw_cutoff = 0.05, lda_cutoff = 2, bootstrap_n = 30, bootstrap_fraction = 2/3, wilcoxon_cutoff = 0.05, multigrp_strat = FALSE, strict = c("0", "1", "2"), sample_min = 10, only_same_subgrp = FALSE, curv = FALSE )
ps |
a |
group |
character, the column name to set the group |
subgroup |
character, the column name to set the subgroup |
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 |
kw_cutoff |
numeric, p value cutoff of kw test, default 0.05 |
lda_cutoff |
numeric, lda score cutoff, default 2 |
bootstrap_n |
integer, the number of bootstrap iteration for LDA, default 30 |
bootstrap_fraction |
numeric, the subsampling fraction value for each
bootstrap iteration, default |
wilcoxon_cutoff |
numeric, p value cutoff of wilcoxon test, default 0.05 |
multigrp_strat |
logical, for multiple group tasks, whether the test is
performed in a one-against one (more strict) or in a one-against all
setting, default |
strict |
multiple testing options, 0 for no correction (default), 1 for independent comparisons, 2 for independent comparison. |
sample_min |
integer, minimum number of samples per subclass for performing wilcoxon test, default 10 |
only_same_subgrp |
logical, whether perform the wilcoxon test only
among the subgroups with the same name, default |
curv |
logical, whether perform the wilcoxon test using the
Curtis's approach, defalt |
a microbiomeMarker object, in which the slot
of
marker_table
contains four variables:
feature
, significantly different features.
enrich_group
, the class of the differential features enriched.
lda
, logarithmic LDA score (effect size)
pvalue
, p value of kw test.
Yang Cao
Segata, Nicola, et al. Metagenomic biomarker discovery and explanation. Genome biology 12.6 (2011): R60.
data(kostic_crc) kostic_crc_small <- phyloseq::subset_taxa( kostic_crc, Phylum == "Firmicutes" ) mm_lefse <- run_lefse( kostic_crc_small, wilcoxon_cutoff = 0.01, group = "DIAGNOSIS", kw_cutoff = 0.01, multigrp_strat = TRUE, lda_cutoff = 4 )