ciseStore-class: Class '"ciseStore"'

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

Description

wrap a BatchJobs registry that manages results of a cis-eQTL search

Objects from the Class

Objects can be created by calls of the form new("ciseStore", reg=reg, ...). All arguments must be named.

We can also use ciseStore(reg, validJobs, addProbeMap = TRUE, addRangeMap = TRUE) and the probemap and rangeMap slots will be populated appropriately. If validJobs is missing, the validJobs slot will be populated by findDone(reg). This may be problematic for handcrafted extracts from archives.

Slots

reg:

Object of class "Registry" BatchJobs Registry instance

validJobs:

Object of class "integer" vector of valid job identifiers for the registry

probemap:

Object of class "data.frame" a map from expression probe identifiers to job identifiers where results for the probe are stored

rangeMap:

Object of class "GRanges" a map from ranges on chromosomes, to job identifiers, in mcols()$jobid

Methods

show

Function describeStore uses batchMapResults and reduceResults to leverage a parallel environment to collect information on numbers of tests and features. Arguments are described in the associated man page.

Note

the construction of the maps occurs via storeApply, which will use foreach, so that registration of a parallel back end using, e.g., registerDoParallel, will determine the speed of construction

Any registry job results that do not inherit from GRanges are mapped to NULL and will not be present in ultimate maps.

Examples

showClass("ciseStore")
# get the global assignment back
require(BatchJobs)
if (require(geuvStore2)) {
 store = makeGeuvStore2()
 store
 }

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