KSomics: Create an KSomics object

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

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

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