RnBeads (version 1.4.0)

run,RnBClusterRun-method: run-methods

Description

Runs the analysis by submitting jobs for each module to the compute cluster

Usage

"run"(object, analysis.id, config.xml, split.differential = TRUE, dry.run = FALSE, long.cmd.thres = 1024L)

Arguments

object

RnBClusterRun object

analysis.id

analysis id. used for naming submitted jobs and log files

config.xml

XML file specifying the analysis options and parameter settings

split.differential

flag indicating whether to split the differnetial methylation module into seperate jobs according to sample annotation column and region type.

dry.run

Prevent the actual job submission. Rather only write to a shell script file

long.cmd.thres

commands that are longer than this number will be encapsulated in shell scripts rather than being submitted as direct command

Value

Nothing of importance

Examples

#specify the xml file for your analysis
xml.file <- "MY_ANALYSIS_SETTINGS.XML"
#set the cluster architecture specific to your environment
arch <- new("ClusterArchitectureSGE")
rnb.cr <- new("RnBClusterRun",arch)
#set up the cluster so that 32GB of memory are required (SGE resource is called "mem_free")
rnb.cr <- setModuleResourceRequirements(rnb.cr,c(mem_free="32G"),"all")
#set up the cluster to use 4 cores on each node for all modules
rnb.cr <- setModuleNumCores(rnb.cr,4L,"all")
#set up the cluster to use 2 cores for the exploratory analysis module
rnb.cr <- setModuleNumCores(rnb.cr,2L,"exploratory")
#run the actual analysis (remove dry.run=TRUE, to really submit the jobs)
run(rnb.cr, "rnbeads_analysis", xml.file, dry.run=TRUE)