get_counts_metadata: get_counts_metadata

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

get_counts_metadata

Description

Check whether the input object is a phyloseq or a TreeSummarizedExperiment, then extract the requested data slots.

Usage

get_counts_metadata(
  object,
  assay_name = "counts",
  min_counts = 0,
  min_samples = 0
)

Arguments

object	a phyloseq or TreeSummarizedExperiment object.
assay_name	the name of the assay to extract from the TreeSummarizedExperiment object (default assayName = "counts"). Not used if the input object is a phyloseq.
min_counts	Parameter to filter taxa. Set this number to keep features with more than min_counts counts in more than min_samples samples (default min_counts = 0).
min_samples	Parameter to filter taxa. Set this number to keep features with a min_counts counts in more than min_samples samples (default min_samples = 0).

Value

a list of results:

• countsthe otu_table slot or assayName assay of the phyloseq or TreeSummarizedExperiment object;

• metadatathe sample_data or colData slot of the phyloseq or TreeSummarizedExperiment object;

• is_phyloseqa boolean equal to TRUE if the input is a phyloseq object.

Examples

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)

mcalgaro93/benchdamic documentation built on Nov. 28, 2022, 6:55 p.m.