run-RnBClusterRun-methods: run-methods

In RnBeads: RnBeads

Description

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

Usage

## S4 method for signature 'RnBClusterRun'
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

Author(s)

Fabian Mueller

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)

RnBeads documentation built on March 3, 2021, 2 a.m.