EMDomics: Create an EMDomics object

Description Usage Arguments Value See Also

View source: R/EMD.R


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


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



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


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


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.


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.


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 "<class 1> vs <class 2>" (e.g. "1 vs 2" or "A vs B").


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


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

See Also


EMDomics documentation built on Nov. 8, 2020, 5:30 p.m.