getWeb: weaveWeb wrapper for the MultiAssayExperiment class

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

weaveWeb wrapper for the MultiAssayExperiment class

Description

weaveWeb wrapper for the MultiAssayExperiment class

Usage

## S4 method for signature 'MultiAssayExperiment'
getWeb(
  x,
  link = NULL,
  ...,
  tableY = NULL,
  tableX = NULL,
  typeY = NULL,
  typeX = NULL,
  force_new = FALSE,
  experiment1 = NULL,
  experiment2 = NULL,
  assay.type1 = NULL,
  assay.type2 = NULL
)

Arguments

x	a MultiAssayExperiment::MultiAssayExperiment().
...	additional parameters passed to AnansiWeb().
link	One of the following: Character scalar with value "none" data.frame with two columns list with two such data.frames
tableY, tableX	⁠Character scalar⁠ or ⁠numeric scalar⁠. Selects experiment corresponding to tableY and tableX from experiments(x) of MultiAssayExperiment object by name or index, name is recommended. (Default slots: Y = 1L, X = 2L).
typeY, typeX	⁠Character scalar⁠ or ⁠numeric scalar⁠. Selects assay from experiments to tableY and tableX from experiments(x). (Default: 1L - the first assay in that experiment).
force_new	boolean If x already has a dictionary Matrix in metadata, ignore it and generate a new object anyway? (Default: FALSE).
experiment1, experiment2	synonymous args to ⁠tableY,tableX⁠ for compatibility with mia argument style.
assay.type1, assay.type2	synonymous args to ⁠typeY,typeX⁠ for compatibility with mia argument style.

Details

This wrapper of weaveWeb() allows to generate an AnansiWeb S4 object directly from objects of class MultiAssayExperiment::MultiAssayExperiment() . First, the assays specified by assay.typeY and assay.typeX are passed to AnansiWeb() to build an AnansiWeb object.

Value

an AnansiWeb object, with sparse binary biadjacency matrix with features from y as rows and features from x as columns in dictionary slot. If x already contains a dictionary in metadata, use that one, unless force_new = TRUE.

Examples

# Make a random anansiWeb
web <- randomWeb()

# Combine experiments into MultiAssayExperiment object
mae <- as(web, "MultiAssayExperiment")

# Back to AnansiWeb
outWeb <- getWeb(mae, tableY = "y", tableX = "x")

thomazbastiaanssen/anansi documentation built on June 9, 2025, 3:59 p.m.