lapplyExec-CommandR-method: lapplyExec-methods

In MPIIComputationalEpigenetics/muPipeR: muPipeR

lapplyExec-methods

Description

lapply for CommandR objects using lexec,CommandR-method

Usage

## S4 method for signature 'CommandR'
lapplyExec(object, X, FUN, env = new.env(parent =
  emptyenv()), loadPackages = .packages(), Rexec = "Rscript",
  name = "run", cleanUp = TRUE, ...)

Arguments

object	CommandR object
X	the object to iterate over. Currently only list objects are supported
FUN	the R function to be run
env	R environment or list storing variables that will be exported and might be used in the function call. Alternatively, it can be a filename of an existing file in which such an environment has been saved using save
loadPackages	character vector of packages to load before executing the function
Rexec	the command that is used to run the R script that is generated
name	a name for the execution that will be used as identifier and prefix for the jobs that are run
cleanUp	should the directory structure created for running the jobs be deleted when completed
...	optional arguments to FUN

Details

It will create an R script for the commands

Value

a list containing the results of FUN for each element in X

Author(s)

Fabian Mueller

Examples

ll <- lapply(1:20,  identity)
cmdr <- CommandRsystem("partest")
rr <- lapplyExec(cmdr, ll, function(i, b){Sys.sleep(1); print(a); print(b); return(paste("success on job", i, "- status:", b))}, env=list(a="success"), Rexec="muRscript", cleanUp=FALSE, b="superduper")
cmdrs <- CommandRslurm("partest", req=c("--partition"="sfgf", "--mem"="4G", "--time"="00:00:10"), user="muellerf")
rr2 <- lapplyExec(cmdrs, ll, function(i, b){Sys.sleep(1); print(a); print(b); return(paste("success on job", i, "- status:", b))}, env=list(a="success"), Rexec="muRscript", cleanUp=FALSE, b="superduper")

MPIIComputationalEpigenetics/muPipeR documentation built on Oct. 18, 2022, 2:35 a.m.