get_counts_metadata | R Documentation |
Check whether the input object is a phyloseq or a TreeSummarizedExperiment, then extract the requested data slots.
get_counts_metadata( object, assay_name = "counts", min_counts = 0, min_samples = 0 )
object |
a phyloseq or TreeSummarizedExperiment object. |
assay_name |
the name of the assay to extract from the
TreeSummarizedExperiment object (default |
min_counts |
Parameter to filter taxa. Set this number to keep features
with more than |
min_samples |
Parameter to filter taxa. Set this number to keep
features with a |
a list
of results:
counts
the otu_table
slot or assayName
assay
of the phyloseq or TreeSummarizedExperiment object;
metadata
the sample_data
or colData
slot of
the phyloseq or TreeSummarizedExperiment object;
is_phyloseq
a boolean equal to TRUE
if the input is
a phyloseq object.
set.seed(1) # Create a very simple phyloseq object counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6) metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"), "group" = as.factor(c("A", "A", "A", "B", "B", "B"))) ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE), phyloseq::sample_data(metadata)) get_counts_metadata(ps) # Or with a TreeSummarizedExperiment tse <- TreeSummarizedExperiment::TreeSummarizedExperiment( assays = list("counts" = counts), colData = metadata) get_counts_metadata(tse)
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