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

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

Value

a vector as ff reference

Details

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

Examples

Run this code

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