storeToFf: extract a vector from store results as ff (out of memory...

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

Description

extract a vector from store results as ff (out of memory reference); support statistical reductions

Usage

storeToFf(store, field, ids = NULL, filter=force, ..., checkField = FALSE,
   ischar=FALSE)

Arguments

store	instance of ciseStore-class
field	character tag, length one. If name of a numeric field in the result set (typically something like 'chisq' in the GRanges generated by cisAssoc), ff is applied directly. Character variables are converted to factors before ff is applied.
ids	job ids to be used; if NULL, process all jobs
filter	function to be applied when GRanges is loaded from results store, should accept and return a GRanges instance
...	supplied to makeRegistry for a temporary registry: typically will be a vector of package names if additional packages are needed to process results
checkField	if TRUE steps will be taken to verify that the tag to which 'field' evaluates is present in result in the first job
ischar	must be true for character vector to be handled properly as a factor, otherwise NA will be returned

Details

uses current BatchJobs configuration to parallelize extraction; reduceResults could be used for a sequential solution

Value

a vector as ff reference

Note

uses ffbase:::c.ff explicitly to concatenate outputs; there is no guarantee of order among elements

Examples

if (require(geuvStore2)) {
 require(BatchJobs)
 store = makeGeuvStore2()
 smchisq = storeToFf( store, "chisq", ids=store@validJobs[1:3]) 
 smchisq
 }

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