BlockExpansion: Attempt to expand blocks of paired features in a...
In npcooley/SynExtend: Tools for Working With Synteny Objects

BlockExpansion

R Documentation

Attempt to expand blocks of paired features in a `PairSummaries` object.

Description

Attempt to expand blocks of paired features in a PairSummaries object.

Usage

BlockExpansion(Pairs,
               GapTolerance = 4L,
               DropSingletons = FALSE,
               Criteria = "PID",
               Floor = 0.5,
               NewPairsOnly = TRUE,
               DBPATH,
               Verbose = FALSE)

Arguments

`Pairs`	An object of class `PairSummaries`.
`GapTolerance`	Integer value indicating the `diff` between feature IDs that can be tolerated to view features as part of the same block. Set by default to `4L`, implying that a single feature missing in a run of pairs will not cause the block to be split. Setting to `3L` would imply that a `diff` of 3 between features, or a gap of 2 features, can be viewed as those features being part of the same block.
`DropSingletons`	Ignore solo pairs when planning expansion routes. Set to `FALSE` by default.
`Criteria`	Either “PID” or “Score”, indicating which metric to use to keep or reject pairs.
`Floor`	Lower PID limit for keeping a pair that was evaluated during expansion.
`NewPairsOnly`	Logical indicating whether or not to return only the pairs that were kept from all expansion attempts, or to return a `PairSummaries` object with the new pairs folded in.
`DBPATH`	A file or connection pointing to the `DECIPHER` database supplied to `FindSynteny` for the original map construction.
`Verbose`	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

BlockExpansion 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.

Value

An object of class PairSummaries.

Author(s)

Nicholas Cooley npc19@pitt.edu

Examples

# this function will be deprecated soon,
# please see the new ExpandDiagonal() function.
library(RSQLite)
DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
                      
data("Endosymbionts_LinkedFeatures", package = "SynExtend")

Pairs <- PairSummaries(SyntenyLinks = Endosymbionts_LinkedFeatures,
                       PIDs = TRUE,
                       Score = TRUE,
                       DBPATH = DBPATH,
                       Verbose = TRUE)
                      
data("Endosymbionts_Pairs01", package = "SynExtend")
Pairs02 <- BlockExpansion(Pairs = Pairs,
                          NewPairsOnly = FALSE,
                          DBPATH = DBPATH,
                          Verbose = TRUE)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.