EMDomics: Create an EMDomics object

In schmolze/EMDomics-devel: Earth Mover's Distance for Differential Analysis of Genomics Data

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 "<class 1> vs <class 2>" (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

schmolze/EMDomics-devel documentation built on May 29, 2019, 3:42 p.m.