R: Class '"refGenome"'

refGenome-class {refGenome} | R Documentation

## Class `"refGenome"`

### Description

refGenome class: Virtual base class for ucscGenome and ensemblGenome.

### Objects from the Class

Objects can be created by calls of the form `refGenome(dbfile)`. dbfile represents SQLite database file.

### Slots

`basedir`:

  Object of class `"character"` Directory where SQLite database is written.

`ev`:

  Object of class `"environment"` Environment that contains data structures. Optionally, there are gtf and attr data.frames.

### Methods

show

  `signature(object = "refGenome")`: Creates a sensible printout.

tableSeqids

  `signature(object = "refGenome")`: Returns tabled seqids which counts all annotations for each seqid. The regex argument will display, which seqid is covered by regex. Intended as preparation for extractSeqids.

extractSeqids

  `signature(object = "refGenome")`: Returns a filtered version of object. Only data for the 'regex' specified seqids is contained. The functions 'ucPrimAssembly' and 'ensPrimAssembly' return regular expressions that allow extraction of primary assemblies for UCSC and Ensembl respectively.

read.gtf

  `signature(object, filename="transcripts.gtf", sep = "\t", useBasedir=TRUE, comment.char = "#", progress=100000L, ...)`: Imports content of gtf file. This is the basic mechanism for data import. It works the same way for ucscGenome and for ensemblGenome.

saveGenome

  `signature(object = "refGenome", filename="character", useBasedir="logical")`: Saves content of all tables to RData file. When useBasedir is set (default), basedir (from basedir-slot) is prefixed.

writeDB

  `signature(object = "refGenome")`: Copies content of gtf, attr and xref table to database.

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## Loading sample data:
    ##-------------------------------------##
    ensfile <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ensfile)
    ens
    ddx <- extractByGeneName(ens,"DDX11L1")
    ddx
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)
    uc
    ddx <- extractByGeneName(uc,"DDX11L1")
    ddx

[Package refGenome version 1.7.7 Index]