PrepareSeqs: Add feature sequences to Decipher databases.
In npcooley/SynExtend: Tools for Working With Synteny Objects

PrepareSeqs

R Documentation

Add feature sequences to Decipher databases.

Description

Given a SynExtend object with a GeneCalls attribute, and a DECIPHER database, add sequence tables named 'AAs' and 'NTs' to the database. The new tables contain all translatable sequences indicated by the genecalls, and all nucleotide feature sequences.

Usage

PrepareSeqs(SynExtendObject,
            DataBase01,
            DefaultTranslationTable = "11",
            Identifiers = NULL,
            Verbose = FALSE)

Arguments

`SynExtendObject`	An object of class `PairSummaries` or of `LinkedPairs`. Object must have a `GeneCalls` attribute.
`DataBase01`	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.
`Verbose`	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

PrepareSeqs adds two tables to a DECIPHER database. One named 'AAs' that contains all translatable features, i.e. features with a coding length divisible by 3 and designated as coding. And another named 'NTs' which contains all features.

Value

An integer count of the number of feature sets added to the DECIPHER database.

Author(s)

Nicholas Cooley npc19@pitt.edu

Examples

DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
                      
data("Endosymbionts_LinkedFeatures", package = "SynExtend")
# this will add seqs to the DB
# PrepareSeqs(SynExtendObject = Endosymbionts_LinkedFeatures,
#             DataBase = DBPATH,
#             Verbose = TRUE)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.