View source: R/ExpandDiagonal.R
ExpandDiagonal | R Documentation |
PairSummaries
object.
Attempt to expand blocks of paired features in a PairSummaries
object.
ExpandDiagonal(SynExtendObject,
FeatureSeqs,
DataBase,
InheritConfidence = TRUE,
GapTolerance = 100L,
DropSingletons = FALSE,
UserConfidence = list("PID" = 0.3),
Verbose = FALSE)
SynExtendObject |
An object of class |
FeatureSeqs |
An object of class |
DataBase |
A character string pointing to a SQLite database, or a connection to a |
InheritConfidence |
A logical indicating whether or not to inheret the user specified column-value pairs assigned to the input object. |
GapTolerance |
Integer value indicating the |
DropSingletons |
Ignore solo pairs when planning expansion routes. Set to |
UserConfidence |
A named list of length 1 where the name identifies a column of the |
Verbose |
Logical indicating whether or not to display a progress bar and print the time difference upon completion. |
ExpandDiagonal
uses a naive expansion algorithm to attempt to fill in gaps in blocks of paired features and to attempt to expand blocks of paired features.
An object of class PairSummaries
.
Nicholas Cooley npc19@pitt.edu
PairSummaries
, NucleotideOverlap
, link{SubSetPairs}
, FindSynteny
DBPATH <- system.file("extdata",
"Endosymbionts_v02.sqlite",
package = "SynExtend")
data("Endosymbionts_LinkedFeatures", package = "SynExtend")
Endosymbiont_Seqs <- PrepareSeqs(SynExtendObject = Endosymbionts_LinkedFeatures,
DataBase = DBPATH,
Verbose = TRUE)
data("Endosymbionts_Pairs02", package = "SynExtend")
Pairs03 <- ExpandDiagonal(SynExtendObject = Endosymbionts_Pairs02,
DataBase = DBPATH,
FeatureSeqs = Endosymbiont_Seqs,
Verbose = TRUE)
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