EMDomics (version 2.2.2)

CVMomics: Create an CVMomics object

Description

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

Usage

CVMomics(data, outcomes, cvm, cvm.perm, pairwise.cvm.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.

cvm

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

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

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

cvm.perm

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

pairwise.cvm.table

A table containing the CVM 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 'CVMomics'. The resulting object is returned.

See Also

calculate_cvm