NucleotideOverlap {SynExtend} | R Documentation

## Tabulating Pairs of Genomic Sequences

### Description

A function for concisely tabulating where genomic features are connected by syntenic hits.

### Usage

    NucleotideOverlap(SyntenyObject,
                      GeneCalls,
                      LimitIndex = FALSE,
                      OutputFormat = "Normal",
                      Verbose = FALSE)

### Arguments

`SyntenyObject` | An object of class “Synteny” built from the `FindSynteny` in the package `DECIPHER`.
`GeneCalls` | A named list of objects of class “DFrame” built from `gffToDataFrame`, objects of class “GRanges” imported from `rtracklayer::import`, or objects of class “Genes” created from the `DECIPHER` function `FindGenes`. “DFrame”s built by “gffToDataFrame” can be used directly, while “GRanges” objects may also be used with limited functionality. Using a “GRanges” object will force all alignments to nucleotide alignments. Objects of class “Genes” generated by `FindGenes` function equivalently to those produced by `gffToDataFrame`. Using a “GRanges” object will force `LimitIndex` to `FALSE`.
`LimitIndex` | Logical indicating whether to limit which indices in a synteny object to query. `FALSE` by default, when `TRUE` only the first sequence in all selected identifiers will be used. `LimitIndex` can be used to skip analysis of plasmids, or solely query a single chromosome.
`OutputFormat` | Character string to designate how much information to return. "Sparse" returns only a filled upper triangle of exactly matched positions. "Normal" returns a matrix with associated match information in both the upper and lower triangle of the returned matrix, while "Comprehensive" will return `GeneCalls` used in construction in the diagonal.
`Verbose` | Logical indicating whether or not to display a progress bar and print the time difference upon completion.

### Details

Builds a matrix of lists that contain information about linked pairs of genomic features.

### Value

An object of class “LinkedPairs”.

### Author(s)

Nicholas Cooley npc19@pitt.edu

### See Also

`FindSynteny`, `Synteny-class`

### Examples

    DBPATH <- system.file("extdata",
                          "VignetteSeqs.sqlite",
                          package = "SynExtend")

    # Alternatively, to build a database using DECIPHER:
    # DBPATH <- tempfile()
    # FNAs <- c("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/006/740/685/GCA_006740685.1_ASM674068v1/GCA_006740685.1_ASM674068v1_genomic.fna.gz",
    #           "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/956/175/GCA_000956175.1_ASM95617v1/GCA_000956175.1_ASM95617v1_genomic.fna.gz",
    #           "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/875/775/GCA_000875775.1_ASM87577v1/GCA_000875775.1_ASM87577v1_genomic.fna.gz")
    # for (m1 in seq_along(FNAs)) {
    #  X <- readDNAStringSet(filepath = FNAs[m1])
    #  X <- X[order(width(X),
    #               decreasing = TRUE)]
    #
    #  Seqs2DB(seqs = X,
    #          type = "XStringSet",
    #          dbFile = DBPATH,
    #          identifier = as.character(m1),
    #          verbose = TRUE)
    # }

    Syn <- FindSynteny(dbFile = DBPATH)

    GeneCalls <- vector(mode = "list",
                        length = ncol(Syn))

    GeneCalls[[1L]] <- gffToDataFrame(GFF = system.file("extdata",
                                                        "GCA_006740685.1_ASM674068v1_genomic.gff.gz",
                                                        package = "SynExtend"),
                                      Verbose = TRUE)
    GeneCalls[[2L]] <- gffToDataFrame(GFF = system.file("extdata",
                                                        "GCA_000956175.1_ASM95617v1_genomic.gff.gz",
                                                        package = "SynExtend"),
                                      Verbose = TRUE)
    GeneCalls[[3L]] <- gffToDataFrame(GFF = system.file("extdata",
                                                        "GCA_000875775.1_ASM87577v1_genomic.gff.gz",
                                                        package = "SynExtend"),
                                      Verbose = TRUE)

    # Alternatively:
    # GeneCalls <- vector(mode = "list",
    #                     length = ncol(Syn))
    # GeneCalls[[1L]] <- rtracklayer::import(system.file("extdata",
    #                                                    "GCA_006740685.1_ASM674068v1_genomic.gff.gz",
    #                                                    package = "SynExtend"))
    # GeneCalls[[2L]] <- rtracklayer::import(system.file("extdata",
    #                                                    "GCA_000956175.1_ASM95617v1_genomic.gff.gz",
    #                                                    package = "SynExtend"))
    # GeneCalls[[3L]] <- rtracklayer::import(system.file("extdata",
    #                                                    "GCA_000875775.1_ASM87577v1_genomic.gff.gz,
    #                                                    package = "SynExtend"))

    names(GeneCalls) <- seq(length(GeneCalls))

    Links <- NucleotideOverlap(SyntenyObject = Syn,
                               GeneCalls = GeneCalls,
                               LimitIndex = FALSE,
                               Verbose = TRUE)

[Package SynExtend version 1.2.0 Index]