EMDomics (version 2.2.2)

KSomics: Create an KSomics object

Description

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

Usage

KSomics(data, outcomes, ks, ks.perm, pairwise.ks.score, pairwise.ks.q = NULL)

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.

ks

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

• ks The calculated KS score.
• q-value The calculated q-value (by permutation analysis).

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

ks.perm

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

pairwise.ks.score

A table containing the KS 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.ks.q

A table of the same dimensions as pairwise.ks.score with the q-values for the pairwise comparisons. Q-values are computed by adjusting the p-value using the Benjamini-Hochberg method within each pairwise comparison.

Value

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

See Also

calculate_ks