EMDomics (version 2.2.2)

EMDomics: Create an EMDomics object

Description

This is the constructor for objects of class 'EMDomics'. It is used in calculate_emd to construct the return value.

Usage

EMDomics(data, outcomes, emd, emd.perm, pairwise.emd.table, pairwise.q.table)

Arguments

data

A matrix containing genomics data (e.g. gene expression levels). The rownames should contain gene identifiers, while the column names should contain sample identifiers.

outcomes

A vector of group labels for each of the sample identifiers. The names of this vector must correspond to the column names of data.

emd

A matrix containing a row for each gene in data, and with the following columns:

• emd The calculated emd score.
• q-value The calculated q-value.

The row names should specify the gene identifiers for each row.

emd.perm

A matrix containing a row for each gene in data, and with a column containing emd scores for each random permutation calculated via calculate_emd.

pairwise.emd.table

A table containing the EMD scores for each pairwise comparison for each gene. For a two-class problem, there should be only one column comparing class 1 and class 2. The row names should be gene identifiers. The column names should be in the format " vs " (e.g. "1 vs 2" or "A vs B").

pairwise.q.table

A table containing the permutation-based q-values for each pairwise comparison for each gene. May be NULL if pairwise.p=F.

Value

The function combines its arguments in a list, which is assigned class 'EMDomics'. The resulting object is returned.

See Also

calculate_emd