Manually Create a pathwayCollection-class Object.

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

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.

Value

A list object with class pathwayCollection.

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.

See also

read_gmt

Examples

  data("colon_pathwayCollection")

  CreatePathwayCollection(
    sets_ls = colon_pathwayCollection$pathways,
    TERMS = colon_pathwayCollection$TERMS
  )
#> Object with Class(es) 'pathwayCollection', 'list' [package 'pathwayPCA'] with 2 elements: 
#>  $ pathways:List of 15
#>  $ TERMS   : chr [1:15] "KEGG_PENTOSE_PHOSPHATE_PATHWAY" ...