NucleotideOverlap {SynExtend} | R Documentation |
A function for concisely tabulating where genomic features are connected by syntenic hits.
NucleotideOverlap(SyntenyObject, GeneCalls, LimitIndex = FALSE, OutputFormat = "Normal", Verbose = FALSE)
SyntenyObject |
An object of class “Synteny” built from the |
GeneCalls |
A named list of objects of class “DFrame” built from |
LimitIndex |
Logical indicating whether to limit which indices in a synteny object to query. |
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 |
Verbose |
Logical indicating whether or not to display a progress bar and print the time difference upon completion. |
Builds a matrix of lists that contain information about linked pairs of genomic features.
An object of class “LinkedPairs”.
Nicholas Cooley npc19@pitt.edu
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)