Check an Input Pathway Collection

Check the class and names of a pathwayCollection object. Add or fix names as appropriate. Add the setsize vector to the object.

CheckPwyColl(pwyColl_ls)

Arguments

pwyColl_ls	A pathway collection supplied to the CreateOmics function

Value

The same pathway collection, but with names modified as described in "Details" and the number of genes per pathway as the setsize element of the collection object.

Details

If there are no names, create them. If there are missing names, label them. If there are duplicated names (because R is stupid and allows duplicate element names in a list---but not a data frame!), then use the data.frame name rule to append a period followed by integers to the end of the name string.

Notes: if the supplied pathways object within your pwyColl_ls list has no names, then this pathway list will be named path1, path2, path3, ...; if any of the pathways are missing names, then the missing pathways will be named noName followed by the index of the pathway. For example, if the 112th pathway in the pathways list has no name (but other pathways do), then this pathway will be named noName112. Furthermore, if any of the pathway names are duplicated, then the duplicates will have .1, .2, .3, ... appended to the duplicate names until all pathway names are unique. Once all pathways have been verified to have unique names, then the pathway names are attached as attributes to the TERMS and setsize vectors (the setsize vector is calculated at object creation).

Examples

 # DO NOT CALL THIS FUNCTION DIRECTLY. CALL FROM WITHIN CreateOmics().

if (FALSE) {
  data("colon_pathwayCollection")
  CheckPwyColl(colon_pathwayCollection)
}