Description Usage Arguments Details Value Methods (by class) Examples
This method lets the user view and set the default values used for the different algorithms in FindMyFriends. Many of the parameters are reoccuring and it can become laborious to type them in at each step. These functionalities makes it easy to set defaults on a per-pangenome basis.
1 2 3 4 5 6 7 8 9 |
object |
A pgVirtual subclass |
value |
The new values to set |
Currently the following methods support reading defaults from a pgVirtual
object. Note that only directly named arguments are supported - arguments
passed on through the ...
-mechanism are not supported unless they are
passed to a function that support it.
graphGrouping
gpcGrouping
variableRegions
plotGroup
kmerLink
plotSimilarity
plotTree
kmerSimilarity
A named list of default values
pgVirtual
: Default values for pgVirtual subclass objects
pgVirtual
: Set defaults for pgVirtual subclass objects
1 2 3 4 5 6 | # Get all object defaults
testPG <- .loadPgExample()
defaults(testPG)
# Set a new default
defaults(testPG)$minFlank <- 2
|
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