storeApply: apply a function over job results in a ciseStore instance

In gQTLBase: gQTLBase: infrastructure for eQTL, mQTL and similar studies

Description

apply a function over job results in a ciseStore instance

Usage

storeApply(store, f, n.chunks, ids=NULL, ..., verbose = FALSE, flatten1=TRUE)

Arguments

store	instance of ciseStore-class
f	function on GRanges stored in ciseStore
n.chunks	Number of chunks into which the jobs are to be broken; the series of chunks is handed to foreach to extract results and apply f to them. If missing, the value of getDoParWorkers() used.
ids	defaults to NULL; if non-null, the jobs to be processed are limited to those identified in this vector.
...	additional arguments to foreach
verbose	if TRUE will allow progressbars and other messages to display
flatten1	if TRUE will execute unlist(...,recursive=FALSE) on output, defaulted to FALSE in previous version

Details

The chunking of job identifiers will determine the degree of parallelization of application, and the form of the list that is returned. flatten1 will eventually default to TRUE.

Value

A list whose structure depends on the chunking of job identifiers. See the examples.

Note

eqtlStore imports BiocParallel's bpparam function, and this determines in real time the number of workers to be employed by storeApply.

See Also

storeMapResults will apply over the store using the batch jobs submission infrastructure and can target specific results via ids; storeApply uses bplapply over the entire store

Examples

if (require(geuvStore2)) {
 require(BatchJobs)
 store = makeGeuvStore2()
 storeApply(store, length)
 storeApply(store, length, ids=c(1:3,603))
 }

gQTLBase documentation built on Nov. 8, 2020, 7:07 p.m.