R: Saving and loading 'refGenome' objects

saveGenome {refGenome} | R Documentation

## Saving and loading `refGenome` objects

### Description

`refGenome` objects contain all annotation data inside an environment. During saving and loading, the whole content of the environment is loaded and saved. The correct object type is also determined in this way.

### Usage

    saveGenome(object,filename,useBasedir=TRUE,...)

### Arguments

`object` | refGenome (or derived)

`filename` | Character. Filename of the R-data-file wich is written.

`useBasedir` | Logical. When TRUE the output file is written into basedir. Otherwise the directory depicted by `dirname(filename)` is used.

`...` | (unused)

### Author(s)

Wolfgang Kaisers

### Examples

    ##-------------------------------------##
    ## A) Ensembl genome
    ##-------------------------------------##
    ensfile <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
    ens <- loadGenome(ensfile)

    saveGenome(ens, "ens.RData", useBasedir=FALSE)

    ## B) Ensembl junctions
    junc <- getSpliceTable(ens)

    saveGenome(junc, "junc.RData", useBasedir=FALSE)
    loadGenome("junc.RData")

    ##-------------------------------------##
    ## C) Ensembl exons
    ##-------------------------------------##
    enex <- refExons(ens)

    saveGenome(enex, "enex.RData", useBasedir=FALSE)
    er <- loadGenome("enex.RData")

    ##-------------------------------------##
    ## D) UCSC genome:
    ##-------------------------------------##
    ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
    uc <- loadGenome(ucfile)

    saveGenome(uc, "uc.RData", useBasedir=FALSE)

    ##-------------------------------------##
    ## E) UCSC junctions
    ##-------------------------------------##
    junc <-getSpliceTable(uc)

    saveGenome(junc, "junc.RData", useBasedir=FALSE)
    jr <- loadGenome("junc.RData")

    ##-------------------------------------##
    ## F) UCSC exons
    ##-------------------------------------##
    ucex <- refExons(uc)

    saveGenome(ucex, "ucex.RData", useBasedir=FALSE)
    ur <- loadGenome("ucex.RData")

[Package refGenome version 1.7.7 Index]