SummarizePairs: Provide summaries of hypothetical orthologs.
In npcooley/SynExtend: Tools for Working With Synteny Objects

SummarizePairs

R Documentation

Provide summaries of hypothetical orthologs.

Description

Given LinkedPairs object and a DECIPHER database, return a data.frame of summarized genomic feature pairs. SummarizePairs will collect all the linked genomic features in the supplied LinkedPairs-class object and return descriptions of the alignments of those features.

Usage

SummarizePairs(SynExtendObject,
               DataBase01,
               IncludeIndexSearch = TRUE,
               AlignmentFun = "AlignPairs",
               RetainAnchors = TRUE,
               DefaultTranslationTable = "11",
               KmerSize = 5,
               IgnoreDefaultStringSet = FALSE,
               Verbose = FALSE,
               ShowPlot = FALSE,
               Processors = 1,
               Storage = 2,
               IndexParams = list("K" = 6),
               SearchParams = list("perPatternLimit" = 1),
               ...)

Arguments

`SynExtendObject`	An object of class `LinkedPairs-class`.
`DataBase01`	A character string pointing to a SQLite database, or a connection to a `DECIPHER` database.
`IncludeIndexSearch`	A logical determining whether to include `SearchIndex` results in the initial inference.
`AlignmentFun`	A character string specifying a `link{DECIPHER}` alignment function. Currently only supports `AlignProfiles` and `AlignPairs`.
`RetainAnchors`	An argument that only affects `AlignPairs`; provide the kmer hits supplied by `FindSynteny` as alignment anchors.
`DefaultTranslationTable`	A character vector of length 1 identifying the translation table to use if one is not supplied in the `GeneCalls` attribute.
`KmerSize`	An integer specifying what Kmer size to collect Kmer distance between sequences at.
`IgnoreDefaultStringSet`	Translate all sequences in nucleotide space.
`Verbose`	Logical indicating whether or not to display a progress bar and print the time difference upon completion.
`ShowPlot`	Logical indicating whether or not to provide a plot of features collected by the function. Currently not implemented.
`Processors`	An integer value indicating how many processors to supply to `AlignPairs`. Supplying `NULL` will cause detection and use of all available cores.
`Storage`	A soft memory limit for how much sequence data from the database to retain in memory while running. In Gb.
`IndexParams`	Arguments to be passed to `IndexSeqs`.
`SearchParams`	Arguments to be passed to `SearchIndex`.
`...`	Additional arguments to pass to interior functions. Currently not implemented.

Details

SummarizePairs collects features describing each linked feature pair. These include an alignment PID, an alignment Score, a Kmer distance, a concensus score for the linking hits –or whether or not linking hits are in similar places in each feature– and a few other 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)
dbDisconnect(DBCONN)
unlink(tmp)

npcooley/SynExtend documentation built on Nov. 15, 2024, 3:02 p.m.