EMDomics: Create an EMDomics object

Description Usage Arguments Value See Also

Description

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

Usage

1
EMDomics(data, samplesA, samplesB, emd, emd.perm)

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.

samplesA

A vector of sample names identifying samples in data that belong to "group A". The names must corresponding to column names in data.

samplesB

A vector of sample names identifying samples in data that belong to "group B". The names must corresponding to column names in data.

emd

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

  • emd The calculated emd score.

  • fc The log2 fold change of "group A" samples relative to "group B" samples.

  • 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.

Value

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

See Also

calculate_emd


schmolze/emd documentation built on May 29, 2019, 3:42 p.m.