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

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

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

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