weaveWebFromTables: Create an anansiWeb object from two 'omics tables and a...

In thomazbastiaanssen/anansi: Annotation-Based Analysis of Specific Interactions

Create an anansiWeb object from two 'omics tables and a dictionary

Description

This function will take two tables of 'omics data, for example metabolomics and functional microbiome data. It will also take a dictionary list, which is provided in this package.

Usage

weaveWebFromTables(
  tableY,
  tableX = NULL,
  dictionary = anansi::anansi_dic,
  verbose = TRUE,
  mode = "interaction",
  prune = FALSE,
  max_sds = 3
)

Arguments

tableY	A table containing features of interest. Rows should be samples and columns should be features. The Y and X refer to the position of the features in a formula: Y ~ X.
tableX	A table containing features of interest. Rows should be samples and columns should be features. The Y and X refer to the position of the features in a formula: Y ~ X. If left empty, tableY will be duplicated.
dictionary	A list that has feature names from tableY as names. Default is the dictionary provided in this package.
verbose	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets.
mode	A character vector. Can be "interaction" or "membership". Toggles whether to link two datasets based on their interactions or based on shared group membership.
prune	A boolean. Toggles whether to prune particularly large groups.
max_sds	A numeric. Only relevant for prune == TRUE. How many SDs larger than the median a group can be before it is pruned. For general use, we recommend sticking to that one. You can access the dictionary like this: data(dictionary)

Value

an anansiWeb object. Web is used as input for most of the main workflow of anansi.

thomazbastiaanssen/anansi documentation built on Feb. 9, 2025, 2:07 p.m.