PairSummaries {SynExtend} | R Documentation |
Takes in a LinkedPairs object and gene calls, and returns a pairs list.
PairSummaries(SyntenyLinks, GeneCalls, DBPATH, PIDs = TRUE, IgnoreDefaultStringSet = FALSE, Verbose = TRUE, GapPenalty = TRUE, TerminalPenalty = TRUE, Model = "Global", Correction = "none")
SyntenyLinks |
A |
GeneCalls |
A named list of objects of class “DFrame” built from |
DBPATH |
A SQLite connection object or a character string specifying the path to the database file. Constructed from DECIPHER's |
PIDs |
Logical indicating whether to perform pairwise alignments. If |
IgnoreDefaultStringSet |
Logical indicating alignment type preferences. If |
Verbose |
Logical indicating whether or not to display a progress bar and print the time difference upon completion. |
GapPenalty |
Argument passed to |
TerminalPenalty |
Argument passed to |
Model |
A character string specifying a model to use to identify pairs that are unlikely to be good orthologs. By default this is ”Global”, but two other models are included; ”Local” and ”Exact”, which have minor differences in performance. Alternatively, a user generated model can be used. |
Correction |
Argument to be passed to |
The LinkedPairs
object generated by NucleotideOverlap
is a container for raw data that describes possible orthologous relationships, however ultimate assignment of orthology is up to user discretion. PairSummaries
generates a clear table with relevant statistics for a user to work with as they choose. The option to align all pairs, though onerous can allow users to apply a hard threshold to predictions by PID, while built in models can allow a more succinct and expedient thresholding.
A data.frame with rownames indicating orthologous pairs.
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) PredictedPairs <- PairSummaries(SyntenyLinks = Links, GeneCalls = GeneCalls, DBPATH = DBPATH, PIDs = FALSE, Verbose = TRUE, Model = "Global", Correction = "none")