OmicsPathway-class {pathwayPCA} | R Documentation

## 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`

[Package pathwayPCA version 1.10.0 Index]