OmicsPathway-class: An S4 class for mass spectrometry or bio-assay data and gene...

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

An S4 class for mass spectrometry or bio-assay data and gene pathway lists

Description

An S4 class for mass spectrometry or bio-assay data and gene pathway lists

Slots

assayData_df

An N \times p data frame with named columns.

sampleIDs_char

A character vector with the N sample names.

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.

trimPathwayCollection

A subset of the list stored in the pathwayCollection slot. This list will have pathways that only contain genes that are present in the assay data frame.

See Also

CreateOmics

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