pathwayCollection-class Object by Pathway.SubsetPathwayCollection.RdThe subset method for pathways lists as returned by the
read_gmt function.
# S3 method for pathwayCollection [[(x, name_char)
| x | An object of class |
|---|---|
| name_char | The name of a pathway in the collection or its unique ID. |
A list of the pathway name (Term), unique ID (pathID),
contents (IDs), description (description), and number of
features (Size).
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.
#> $Term #> [1] "KEGG_RETINOL_METABOLISM" #> #> $PathID #> [1] "pathway60" #> #> $IDs #> [1] "RPE65" "CYP3A5" "UGT2B28" "CYP4A11" "CYP3A4" "RDH8" "DHRS3" #> [8] "CYP2C18" "ADH1B" "ADH1C" "ADH4" "ADH5" "DGAT2" "ADH1A" #> [15] "BCMO1" "RDH10" "CYP26A1" "UGT2B11" "CYP2C9" "AWAT2" "CYP26C1" #> [22] "CYP2C19" "CYP2C8" "CYP2B6" "UGT2A3" "CYP2A13" "UGT1A4" "CYP3A7" #> [29] "UGT1A1" "UGT1A3" "CYP26B1" "DHRS9" "UGT1A10" "DGAT1" "UGT1A8" #> [36] "UGT1A7" "UGT1A6" "ALDH1A1" "RETSAT" "RDH12" "LRAT" "RDH11" #> [43] "UGT1A5" "CYP2A6" "CYP2A7" "CYP4A22" "DHRS4" "CYP1A1" "CYP1A2" #> [50] "ADH7" "ADH6" "UGT2A1" "ALDH1A2" "CYP3A43" "DHRS4L2" "RDH16" #> [57] "UGT1A9" "RDH5" "UGT2B10" "UGT2B7" "PNPLA4" "UGT2B4" "UGT2B17" #> [64] "UGT2B15" #> #> $Description #> [1] NA #> #> $Size #> [1] 64 #>