NucleotideOverlap: Tabulating Pairs of Genomic Sequences

In SynExtend: Tools for Working With Synteny Objects

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 [e-mail]

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)

SynExtend documentation built on Nov. 8, 2020, 7:50 p.m.