app2gds {bigmelon} | R Documentation

## Append a MethyLumiSet object to a CoreArray Genomic Data Structure (GDS) data file

### Description

This function will append a MethyLumiSet data object to a CoreArray Genomic Data Structure(GDS) data file, and return as a gds.class object.

### Usage

    app2gds(m, bmln)

### Arguments

`m` | The MethyLumiSet object to be appended to the CoreArray Genomic Data Structure (GDS) data file
`bmln` | Either: A gds.class object Or: A character string specifying the name of an existing .gds file to write to. Or: A character string specifying the name of a new .gds file to write to

### Details

Currently, the function only works with MethylumiSet objects and will produce unexpected results if the number of rows of the new objects does not match the existing .gds object. To prevent any errors from occuring it is recommended that raw .idat files are read in with `readEPIC` or appended `iadd` to ensure that all rows are the same length and have the same annotation.

### Value

A gds.class object, which points to the appended .gds file.

### Author(s)

Leonard C Schalkwyk, Ayden Saffari, Tyler Gorrie-Stone Who to contact: <tgorri@essex.ac.uk>

### See Also

`es2gds`, `iadd`.

### Examples

    #load example dataset
    data(melon)

    #split data into halves
    melon_1 <- melon[,1:6]
    melon_2 <- melon[,7:12]

    #convert first half to gds
    e <- es2gds(melon_1,'1_half_melon.gds')

    #append second half to existing gds file
    f <- app2gds(melon_2,e)

    closefn.gds(e)
    unlink("1_half_melon.gds")

[Package bigmelon version 1.12.0 Index]