Description Usage Arguments Details Value Examples
The subset method for pathways lists as returned by the
read_gmt
function.
1 2 | ## S3 method for class 'pathwayCollection'
x[[name_char]]
|
x |
An object of class |
name_char |
The name of a pathway in the collection or its unique ID. |
This function finds the index matching the name_char
argument
to the TERMS
field of the pathwayCollection
-class Object,
then subsets the pathways
list, TERMS
vector,
description
vector, and setsize
vector by this index. If you
subset a trimmed pathwayCollection
object, and the function errors
with "Pathway not found.", then the pathway specified has been trimmed
from the pathway collection.
Also, this function does not allow for users to overwrite any portion of
a pathway collection. These objects should rarely, if ever, be changed.
If you absolutely must change the components of a pathwayCollection
object, then create a new one with the codeCreatePathwayCollection
function.
A list of the pathway name (Term
), unique ID (pathID
),
contents (IDs
), description (description
), and number of
features (Size
).
1 2 | data("colon_pathwayCollection")
colon_pathwayCollection[["KEGG_RETINOL_METABOLISM"]]
|
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