run_lefse  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 oneagainst one (more strict) or in a oneagainst 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.
normalize
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
)
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