Description Usage Functions See Also Examples
View source: R/transform-filter.R
Wrappers around phyloseq::filter_taxa that allow using a purrr-style
anonymous function for .f
.
1 2 3 | filter_taxa(physeq, .f, prune = FALSE)
filter_taxa2(physeq, .f)
|
filter_taxa2
: Sets prune = TRUE
phyloseq::filter_taxa tidyseq::transform_sample_counts
1 2 3 4 5 6 7 | library(phyloseq)
library(tidyseq)
data(GlobalPatterns)
# Filter low prevalence taxa and then convert to proportions
gp.prop <- GlobalPatterns %>%
filter_taxa2(~ sum(. > 0) > 5) %>%
transform_sample_counts(~ . / sum(.))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.