CreatePathwayCollection {pathwayPCA} | R Documentation

## Manually Create a `pathwayCollection`-class Object.

### Description

Manually create a `pathwayCollection` list similar to the output of the `read_gmt` function.

### Usage

    CreatePathwayCollection(sets_ls, TERMS, setType = c("pathways", "genes",
      "regions"), ...)

### Arguments

`sets_ls` | A named list of character vectors. Each vector should contain the names of the individual genes, proteins, sits, or CpGs within that set as a vector of character strings. If you create this pathway collection to integrate with data of class `Omics`*, the names contained in these vectors should have non-empty overlap with the feature names of the assay data frame that will be paired with this list in the subsequent analysis.
`TERMS` | A character vector the same length as the `sets_ls` list with the proper names of the sets.
`setType` | What is the type of the set: pathway set of gene, gene sites in RNA or DNA, or regions of CpGs. Defaults to `''pathway''`.
`...` | Additional vectors or data components related to the `sets_ls` list. These values should be passed as a name-value pair. See "Details" for more information.

### Details

This function checks the set list and set term inputs and then creates a `pathwayCollection` object from them. Pass additional list elements (such as the `description` of each set) using the form `tag = value` through the `...` argument (as in the `list` function). Because some functions in the `pathwayPCA` package add and edit elements of `pathwayCollection` objects, please do not create `pathwayCollection` list items named `setsize` or `n_tested`.

### Value

A list object with class `pathwayCollection`.

### See Also

`read_gmt`

### Examples

      data("colon_pathwayCollection")

      CreatePathwayCollection(
        sets_ls = colon_pathwayCollection$pathways,
        TERMS = colon_pathwayCollection$TERMS
      )

[Package pathwayPCA version 1.2.0 Index]