iadd {bigmelon}R Documentation

Add data from IDAT files for a single barcode to a gds file

Description

Add data from IDAT files for a single barcode to a gds file. or Add data from many IDAT files from a single directory to a gds file.

Usage

iadd(bar, gds,...)
iadd2(path, gds, chunksize = NULL, ...)

Arguments

bar

The barcode for an IDAT file Or the file path of the file containing red or green channel intensities for that barcode (this will automatically locate and import both files regardless of which one you provide)

path

The file path where (multiple) IDAT files exist. Iadd2 will process every idat within the specified directory.

gds

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

chunksize

If NULL, iadd2 will read in all barcodes in one go. Or if supplied with a numeric value, iadd2 will read in that number of idat files in batches

...

Additional Arguments passed to methylumIDATepic.

Value

returns a gds.class object, which points to the appended .gds file.

Author(s)

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

See Also

es2gds, app2gds.

Examples

if(require('minfiData')){
bd <- system.file('extdata', package='minfiData')
gfile <- iadd2(file.path(bd, '5723646052'), gds = 'melon.gds')
closefn.gds(gfile)
unlink('melon.gds')
}

[Package bigmelon version 1.6.0 Index]