LUPINE for single time point

LUPINE for single time point

Usage

LUPINE_single(
  data,
  day,
  excluded_taxa = NULL,
  is.transformed = FALSE,
  lib_size = NULL,
  method = "pca",
  ncomp = 1
)

Arguments

data

A 3D array of counts or transformed data with dimensions samples x taxa x time points

day

The time point for which the correlations are calculated

excluded_taxa

A list of taxa to be excluded at each time point

is.transformed

A logical indicating whether the data is transformed or not

lib_size

A matrix of library sizes for each sample and time point

method

The method to use for dimensionality reduction. Options are "pca", "ica", "rpca"

ncomp

The number of components to use for dimensionality reduction

Value

A list of correlations and p-values