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

ExpandDiagonal

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

ExpandDiagonal(SynExtendObject,
               DataBase01,
               InheritConfidence = FALSE,
               GapTolerance = 100L,
               DropSingletons = FALSE,
               UserConfidence = list("PID" = 0.3),
               Processors = 1,
               Verbose = FALSE)

Arguments

`SynExtendObject`	An object of class `PairSummaries`.
`DataBase01`	A character string pointing to a SQLite database, or a connection to a `DECIPHER` database.
`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 `diff` between feature IDs that can be tolerated to view features as part of the same block. Set by default to `100L`.
`DropSingletons`	Ignore solo pairs when planning expansion routes. Set to `FALSE` by default.
`UserConfidence`	A named list of length 1 where the name identifies a column of the `PairSummaries` object, and the value identifies a user confidence. To be retained, a pair evaluated for expansion must be above all user specified confidences.
`Processors`	An integer value indicating how many processors to supply to `AlignPairs`. Supplying `NULL` will cause detection and use of all available cores.
`Verbose`	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

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.

Value

An object of class PairSummaries.

Author(s)

Nicholas Cooley npc19@pitt.edu

Examples

library(RSQLite)
DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
tmp <- tempfile()
system(command = paste("cp",
                       DBPATH,
                       tmp))
DBCONN <- dbConnect(SQLite(), tmp)
                      
data("Endosymbionts_LinkedFeatures", package = "SynExtend")
PrepareSeqs(SynExtendObject = Endosymbionts_LinkedFeatures,
            DataBase01 = DBCONN,
            Verbose = TRUE)
SummarizedPairs <- SummarizePairs(SynExtendObject = Endosymbionts_LinkedFeatures,
                                  DataBase01 = DBCONN,
                                  Verbose = TRUE)
ExpandedPairs <- ExpandDiagonal(SynExtendObject = SummarizedPairs,
                                DataBase01 = DBCONN,
                                Verbose = TRUE)
dbDisconnect(DBCONN)
unlink(tmp)

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