storeMapResults: use batchMapResults infrastructure to process results in a...

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

Description

use batchMapResults infrastructure to process results in a ciseStore instance

Usage

storeMapResults(store, reg2, fun, ..., 
    ids = NULL, part = NA_character_, more.args = list())
loadAndFilterResult(reg, 
 id, filter=force, part = NA_character_, missing.ok = FALSE)

Arguments

store	an instance of ciseStore-class
reg	instance of BatchJobs Registry class
reg2	an empty instance of the Registry class (see makeRegistry)
fun	A function to map over results in store, with formals (job, res, ...).
filter	a function that accepts and returns a GRanges instance, to be applied just after loading a result from the store
...	additional arguments to vectorize over (should be same length as length(findDone(store@reg))
ids	ids of job results to be mapped; if missing, map all job results
id	a single job id
part	see batchMapResults
missing.ok	see loadResult
more.args	a list of other arguments to be passed to fun; default is empty list.

Value

integer vector with job ids. Main purpose is to prepare the registry for submitJobs.

Note

loadAndFilterResult is not intended to be exported and may be removed in future versions.

Author(s)

VJ Carey <[e-mail]>

Examples

## Not run: 
if (require(geuvStore2)) {
 require(BatchJobs)
 store = makeGeuvStore2()
 fd = tempfile()
 tempreg = makeRegistry("tempSMR", file.dir=fd)
 storeMapResults( store, tempreg, fun=function(job, res, ...) length(res) )
 showStatus(tempreg)
 submitJobs(tempreg, 1:2)
 loadResults(tempreg)
 unlink(fd)
 }

## End(Not run)

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