OmicsCateg-class: An S4 class for categorical responses within an...

In pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Description

This creates the OmicsCateg class which extends the OmicsPathway master class.

Slots

assayData_df

An N \times p data frame with named columns.

pathwayCollection

A list of known gene pathways with three or four elements:

• pathways : A named list of character vectors. Each vector contains the names of the individual genes within that pathway as a vector of character strings. The names contained in these vectors must have non-empty overlap with the column names of the assayData_df data frame. The names of the pathways (the list elements themselves) should be the a shorthand representation of the full pathway name.

• TERMS : A character vector the same length as the pathways list with the proper names of the pathways.

• description : An optional character vector the same length as the pathways list with additional information about the pathways.

• setsize : A named integer vector the same length as the pathways list with the number of genes in each pathway. This list item is calculated during the creation step of a CreateOmics function call.

response

A factor vector of length N: the dependent variable of a generalized linear regression exercise. Currently, we support binary factors only. We expect to extend support to n-ary responses in the next package version.

See Also

OmicsPathway, CreateOmics

pathwayPCA documentation built on Dec. 15, 2020, 6:14 p.m.