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

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

An S4 class for categorical responses within an OmicsPathway object

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

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.