iadd: Add data from Illumina IDAT files to a gds file.

In TJGorrie/bigmelon: Illumina methylation array analysis for large experiments

Add data from Illumina IDAT files to a gds file.

Description

iadd will add data from multiple, specified, idat files providing '/path/to/barcode' is valid path to a specified gds file. Barcode here implies the first part of the idat file name i.e without '_(Red|Grn).idat'

iadd2 will add data from all idat files that are stored within a single directory to a gds file.

idats2gds will add data from a set of barcodes into the same gds file, one by one, optionally will handle idat files from different maps providing force=TRUE. However, will not combine from arrays of differing types e.g. 450k vs EPIC.

Usage

iadd(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, ...)
iadd2(path, gds, chunksize = NULL, force=TRUE, ...)
idats2gds(barcodes, gds, n=TRUE, force = FALSE, ...)

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
n	Logical, whether or not bead-counts are extracted from idat files.
force	Logical, whether or not rownames from the first idat file are applied to all idat files. Useful in combining together idat files of differing lengths.
target_cpgs	A vector of CpGs to specifically read in and set the dimensions of array to.
barcodes	A vector of barcodes to load into an existing gds file.
...	Additional Arguments passed to wateRmelons 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: <[e-mail]>

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')
}

TJGorrie/bigmelon documentation built on Oct. 13, 2023, 9:51 p.m.