PrepareSeqs: Return gene sequences.
In npcooley/SynExtend: Tools for Working With Synteny Objects

PrepareSeqs

R Documentation

Return gene sequences.

Description

Given a SynExtend object with a GeneCalls attribute, and a DECIPHER database, return all gene sequences and their translations.

Usage

PrepareSeqs(SynExtendObject,
            DataBase,
            DefaultTranslationTable = "11",
            Identifiers = NULL,
            Storage = 1,
            Verbose = FALSE)

Arguments

`SynExtendObject`	An object of class `PairSummaries` or of `LinkedPairs`. Object must have a `GeneCalls` attribute.
`DataBase`	A character string pointing to a SQLite database, or a connection to a `DECIPHER` database.
`DefaultTranslationTable`	A character vector of length 1 identifying the translation table to use if one is not supplied in the `GeneCalls` attribute.
`Identifiers`	By default `NULL`, but can be used to supply a vector of character identifiers for returning a subset of prepared sequences.
`Storage`	A soft memory limit for how much space to allow when building the resulting object. Translated to Gb.
`Verbose`	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

PrepareSeqs returns the sequences of genes and their translations where appropriate.

Value

An object of class FeatureSeqs.

Author(s)

Nicholas Cooley npc19@pitt.edu

Examples

DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
                      
data("Endosymbionts_LinkedFeatures", package = "SynExtend")
CurrentSeqs <- PrepareSeqs(SynExtendObject = Endosymbionts_LinkedFeatures,
                           DataBase = DBPATH,
                           Verbose = TRUE)

npcooley/SynExtend documentation built on May 2, 2024, 7:28 p.m.