README.md

In SynExtend: Tools for Working With Synteny Objects

SynExtend

Table of contents:

Introduction Installation Usage Reporting Bugs and Errors

Introduction

SynExtend is a package of tools for working with synteny objects generated from the Bioconductor Package DECIPHER.

Installation

SynExtend is currently in the submission process to Bioconductor and will be be available there upon acceptance, until then it can be installed from this repository via:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

BiocManager::install("SynExtend")
library("SynExtend")

Additionally, SynExtend is maintained in a Docker container at: Coming Soon!

Usage

Currently SynExtend's major function is facilitating the prediction of orthologous gene pairs from synteny maps. The functions herein rely on synteny maps built by the FindSynteny function in the package DECIPHER. The process is relatively straightforward and only requires assemblies and genecalls, which can be conveniently pulled from the NCBI using entrez. However, as long as given assemblies have associated gene calls, or can have gene calls generated, they will work just fine.

Using entrez, this process would start like this:

library(SynExtend)

EntrezQuery <- paste("esearch -db assembly ",
                     "-query '",
                     "thaumarchaeota[organism] ",
                     'AND "complete genome"[filter] ',
                     'AND "genbank has annotation"[properties] ',
                     "NOT anomalous[filter]' ",
                     '| ',
                     'esummary ',
                     '| ',
                     'xtract -pattern DocumentSummary -element FtpPath_GenBank',
                     sep = "")

FtPPaths <- system(command = EntrezQuery,
                   intern = TRUE,
                   timeout = 300L) # timeout argument is required for RStudio only

FNAs <- unname(sapply(FtPPaths,
                      function(x) paste(x,
                                        "/",
                                        strsplit(x,
                                                 split = "/",
                                                 fixed = TRUE)[[1]][10],
                                        "_genomic.fna.gz",
                                        sep = "")))

GFFs <- unname(sapply(FtPPaths,
                      function(x) paste(x,
                                        "/",
                                        strsplit(x,
                                                 split = "/",
                                                 fixed = TRUE)[[1]][10],
                                        "_genomic.gff.gz",
                                        sep = "")))

With these matched character vectors describing files on the NCBI FTP site, we can pull given assemblies, and their associated genecalls.

Assemblies are pulled using functions within the package Biostrings and placed in a sqlite database using the package DECIPHER. Note, DBPATH can be a specific local file location, though a tempfile works fine for this example. The tempfile in this example will be destroyed upon closure of the current R session, so specified files are preferable for most user activity.

DBPATH <- tempfile()

for (m1 in seq_along(FNAs)) {
  X <- readDNAStringSet(FNAs[m1])
  X <- X[order(width(X),
               decreasing = TRUE)]
  Seqs2DB(seqs = X,
          type = "XStringSet",
          dbFile = DBPATH,
          identifier = as.character(m1),
          verbose = TRUE)
}

A function within the package SynExtend allows us to import GFF3 formatted gene annotations into a simple data.frame, and names are added to this generated list for later use.

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

for (m1 in seq_along(GFFs)) {
  GeneCalls[[m1]] <- gffToDataFrame(GFF = GFFs[m1],
                                    Verbose = TRUE)

}

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

A synteny object is generated.

Syn <- FindSynteny(dbFile = DBPATH)

Genecalls are overlaid on the synteny map.

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

And positions on the grid of gene calls that are occupied by syntenic hits are recorded, and evaluated with a simple model to remove poor links. The function PairSummaries has arguments allowing a user align, and collect PIDs for each predicted pair, but that step is generally too cumbersome for a README example.

PairedGenes <- PairSummaries(SyntenyLinks = Links,
                             GeneCalls = GeneCalls,
                             DBPATH = DBPATH,
                             PIDs = FALSE,
                             Model = "Global",
                             Verbose = TRUE)

A more self-contained example is maintained in this package's Bioconductor vignette, and can be found here: ...

Reporting Bugs and Errors

Feel free to email me at [e-mail], or submit bugs here on github.

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