AnansiWeb S7 container class

AnansiWeb is an S7 class containing two feature tables as well as a dictionary to link them. AnansiWeb is the main container that will hold your input data throughout the anansi pipeline.

Typical use of the anansi package will involve generating an AnansiWeb object using the weaveWeb() function.

The function AnansiWeb() constructs an AnansiWeb object from two feature tables and an adjacency matrix.

Usage

## Constructor for `AnansiWeb` objects
AnansiWeb(tableX, tableY, dictionary, metadata = data.frame())

Arguments

tableY, tableX

A table containing features of interest. Rows should be samples and columns should be features. Y and X refer to the position of the features in a formula: Y ~ X.

dictionary

A binary adjacency matrix of class Matrix, or coercible to Matrix

metadata

list of metadata. Optional.

Value

an AnansiWeb object, with sparse binary biadjacency matrix with features from y as rows and features from x as columns in dictionary slot.

Slots

tableY,tableX

Two matrix objects of measurements, data. Rows are samples and columns are features. Access with @tableY and @tableX.

dictionary

Matrix, binary adjacency matrix. Optionally sparse. Typically generated using the weaveWeb() function. Access with @dictionary.

metadata

Optional data.frame of sample metadata. Access with @metadata.

See also

• AnansiWeb-methods

• randomAnansi: For generation of random AnansiWeb objects.

• kegg_link(): For examples of input for link argument.

Examples

# Use AnansiWeb() to construct an AnansiWeb object from components:
tX <- `dimnames<-`(replicate(5, (rnorm(36))),
    value = list(
        as.character(seq_len(36)),
        letters[1:5]
    )
)
tY <- `dimnames<-`(replicate(3, (rnorm(36))),
    value = list(
        as.character(seq_len(36)),
        LETTERS[1:3]
    )
)

d <- matrix(TRUE,
    nrow = NCOL(tY), ncol = NCOL(tX),

    # Note: Dictionary should have named dimensions
    dimnames = list(
        y_names = colnames(tY),
        x_names = colnames(tX)
    )
)
web <- AnansiWeb(tableX = tX, tableY = tY, dictionary = d)
#> Warning: Argument `metadata` not provided; Please validate sample ID order.