SummarizePairs: Provide summaries of hypothetical orthologs.

In npcooley/SynExtend: Tools for Working With Synteny Objects

Provide summaries of hypothetical orthologs.

Description

Given the correct set of SynExtend objects 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,
               FeatureSeqs,
               DataBase,
               AlignmentFun = "AlignProfiles",
               RetainAnchors = FALSE,
               DefaultTranslationTable = "11",
               KmerSize = 5,
               IgnoreDefaultStringSet = FALSE,
               Verbose = FALSE,
               ShowPlot = FALSE,
               Processors = 1,
               ...)

Arguments

SynExtendObject	An object of class LinkedPairs-class.
FeatureSeqs	An object of class FeatureSeqs.
DataBase	A character string pointing to a SQLite database, or a connection to a DECIPHER database.
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	A soft memory limit for how much space to allow when building the resulting object. Translated to Gb.
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.
Processors	An integer value indicating how many processors to supply to AlignPairs.
...	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 [e-mail]

See Also

PrepareSeqs, NucleotideOverlap, FindSynteny, LinkedPairs-class

Examples

DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
                      
data("Endosymbionts_LinkedFeatures", package = "SynExtend")
Endosymbiont_Seqs <- PrepareSeqs(SynExtendObject = Endosymbionts_LinkedFeatures,
                                 DataBase = DBPATH,
                                 Verbose = TRUE)
SummarizedPairs <- SummarizePairs(SynExtendObject = Endosymbionts_LinkedFeatures,
                                  FeatureSeqs = Endosymbiont_Seqs,
                                  DataBase = DBPATH)
                           

npcooley/SynExtend documentation built on May 17, 2024, 1:50 p.m.