ExtractBy {SynExtend}R Documentation

Extract and organize XStringSets of sequences represented in a PairSummaries object.

Description

Takes in a PairSummaries object and an optional vector of cluster representatives. Return an XStringSet of the sequences present in the PairSummaries, or when cluster representatives are provided, a list of XStringSets of the sequences that make up the provided clusters.

Usage

ExtractBy(x,
          y = NULL,
          DBPATH,
          Method = "all",
          DefaultTranslationTable = "11",
          Translate = TRUE,
          Storage = 1,
          Verbose = FALSE)

Arguments

x

A PairSummaries object.

y

An optional list containing the ids of sequences in the PairSummaries object.

DBPATH

A SQLite connection object or a character string specifying the path to the database file. Constructed from DECIPHER's Seqs2DB function.

Method

How to extract sequences from the PairSummaries object. Currently only the methods “all” and “clusters” are supported.

Translate

If TRUE return AAStringSets where possible.

DefaultTranslationTable

Currently Not Implemented! When implemented will allow for designation of a specific translation table if one is not indicated in the GeneCalls attribute of the PairSummaries object.

Storage

Numeric indicating the approximate size a user wishes to allow for holding StringSets in memory to extract gene sequences, in “Gigabytes”. The lower Storage is set, the more likely that ExtractBy will need to reaccess StringSets when extracting gene sequences. The higher Storage is set, the more sequences ExtractBy will attempt to hold in memory, avoiding the need to re-access the source database many times. Set to 1 by default, indicating that ExtractBy can store a “Gigabyte” of sequences in memory at a time.

Verbose

Logical indicating whether to print progress bars and messages. Defaults to FALSE.

Details

Takes in a PairSummaries object and an optional vector of cluster representatives. Return an XStringSet of the sequences present in the PairSummaries, or when cluster representatives are provided, a list of XStringSets of the sequences that make up the provided clusters.

Value

Returns either a XStringSet or a list of XStringSets.

Author(s)

Nicholas Cooley npc19@pitt.edu

See Also

FindSynteny, Synteny-class, PairSummaries, DisjointSet

Examples

DBPATH <- system.file("extdata",
                      "VignetteSeqs.sqlite",
                      package = "SynExtend")
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)
names(GeneCalls) <- seq(length(GeneCalls))
Links <- NucleotideOverlap(SyntenyObject = Syn,
                           GeneCalls = GeneCalls,
                           LimitIndex = FALSE,
                           Verbose = TRUE)
PredictedPairs <- PairSummaries(SyntenyLinks = Links,
                                DBPATH = DBPATH,
                                PIDs = FALSE,
                                AcceptContigNames = TRUE,
                                Verbose = TRUE)
PresentSeqs <- ExtractBy(x = PredictedPairs,
                         Method = "all",
                         DBPATH = DBPATH,
                         Verbose = TRUE)
Clusters <- DisjointSet(Pairs = PredictedPairs,
                        Verbose = TRUE)
SeqsByClusters <- ExtractBy(x = PredictedPairs,
                            y = Clusters,
                            Method = "clusters",
                            DBPATH = DBPATH,
                            Verbose = TRUE)

# Alternatively the same seqs can be accessed from the NCBI FTP site
# And gene calls can be accessed with the rtracklayer
## Not run: 
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)
  }

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,
                                DBPATH = DBPATH,
                                PIDs = FALSE,
                                AcceptContigNames = TRUE,
                                Verbose = TRUE)
PresentSeqs <- ExtractBy(x = PredictedPairs,
                         Method = "all",
                         DBPATH = DBPATH,
                         Verbose = TRUE)
Clusters <- DisjointSet(Pairs = PredictedPairs,
                        Verbose = TRUE)
SeqsByClusters <- ExtractBy(x = PredictedPairs,
                            y = Clusters,
                            Method = "clusters",
                            DBPATH = DBPATH,
                            Verbose = TRUE)

## End(Not run)
[Package SynExtend version 1.4.1 Index]