oligo (version 1.36.1)

ldSetOptions: Set/check large dataset options.

Description

Set/check large dataset options.

Usage

ldSetOptions(nsamples=100, nprobesets=20000, path=getwd(), verbose=FALSE)
ldStatus(verbose=FALSE)
ldPath(path)

Arguments

nsamples

number of samples to be processed at once.

nprobesets

number of probesets to be processed at once.

path

path where to store large dataset objects.

verbose

verbosity (logical).

Details

Some functions in oligo/crlmm can process data in batches to minimize memory footprint. When using this feature, the 'ff' package resources are used (and possibly combined with cluster resources set in options() via 'snow' package).

Methods that are executed on a sample-by-sample manner can use ocSamples() to automatically define how many samples are processed at once (on a compute node). Similarly, methods applied to probesets can use ocProbesets(). Users should set these options appropriately.

ldStatus checks the support for large datasets.

ldPath checks where ff files are stored.

See Also

ocSamples, ocProbesets

Examples

ldStatus(TRUE)