collapseParalogues {FindMyFriends} | R Documentation |
This method allows for merging of paralogue gene groups defined using
kmerLink
into new, bigger, gene groups.
collapseParalogues(object, ...) ## S4 method for signature 'pgVirtual' collapseParalogues(object, combineInfo = "merge", ...)
object |
A pgVirtual subclass |
... |
parameters passed on to metadata collapse function. For combineInfo='merge' sep specifies the separator - sep='none' collapses information into list elements instead of strings. For combineInfo='largest' no addition arguments are given. |
combineInfo |
The approach used to combine metadata from the collapsed groups. Either 'merge' for merging, 'largest' for picking information from the largest group, or a function that takes a data.frame of multiple rows and converts it to a data.frame with one row and the same columns. |
An object of the same class as object with the new grouping.
pgVirtual
: Merge paralogue gene groups for all pgVirtual
subclasses
testPG <- .loadPgExample(withGroups=TRUE, withParalogues=TRUE) # Number of gene groups before collapse nGeneGroups(testPG) # Number of gene groups after collapse testPG <- collapseParalogues(testPG, combineInfo='largest') nGeneGroups(testPG)