View source: R/transform-filter.R
filter_taxa | R Documentation |
Variations of phyloseq::filter_taxa()
that allows a purrr-style anonymous
function.
filter_taxa(physeq, fun, prune = FALSE)
filter_taxa2(physeq, fun)
physeq |
|
fun |
A function or formula that can be converted to a function by
|
prune |
A logical. If |
filter_taxa()
simply calls purrr::as_mapper()
on fun
and passes the
resulting function on to phyloseq::filter_taxa()
. filter_taxa2()
also
sets prune = TRUE
, which is convenient when passing a phyloseq object in a
pipe chain (see example).
filter_taxa2()
: Sets prune = TRUE
phyloseq::filter_taxa()
purrr::as_mapper()
data(GlobalPatterns)
# Filter low prevalence taxa and then convert to proportions
gp.prop <- GlobalPatterns %>%
filter_taxa2(~ sum(. > 0) > 5) %>%
transform_sample_counts(~ . / sum(.))
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