SeqArray (version 1.8.0)

seqParallel: Apply Functions in Parallel

Description

Apply a user-defined function in parallel

Usage

seqParallel(cl, gdsfile, FUN = function(gdsfile, ...) NULL,
	split=c("by.variant", "by.sample", "none"), .combine=NULL, ...)

Arguments

cl

NULL or a cluster object, created by the package parallel or snow

gdsfile

a SeqVarGDSClass object

FUN

the function to be applied

split

split the dataset by variant or sample according to multiple processes, or "none" for no split

.combine

define a fucntion for combining results from different processes; by default, 'c' is used; if .combine=="", return invisible()

...

optional arguments to FUN

Value

A vector or list of values.

Details

If cl = NULL or length(cl) == 0, the function simply calls FUN(gdsfile, ...); otherwise, it splits jobs to different processes and calls FUN(gdsfile, ...) on each process, the optional arguments are passed to different processes.

See Also

seqSetFilter, seqGetData seqApply

Examples

library(parallel)

# Use option cl.core to choose an appropriate cluster size or number of cores
cl <- makeCluster(getOption("cl.cores", 2))


# the file of GDS
gds.fn <- seqExampleFileName("gds")
# or gds.fn <- "C:/YourFolder/Your_GDS_File.gds"

# display
(f <- seqOpen(gds.fn))

# the uniprocessor version
afreq1 <- seqParallel(NULL, f, FUN = function(gdsfile) {
		seqApply(gdsfile, "genotype", as.is="double",
			FUN=function(x) mean(x==0, na.rm=TRUE))
	}, split = "by.variant")

length(afreq1)
summary(afreq1)


# run in parallel
afreq2 <- seqParallel(cl, f, FUN = function(gdsfile) {
		seqApply(gdsfile, "genotype", as.is="double",
			FUN=function(x) mean(x==0, na.rm=TRUE))
	}, split = "by.variant")

length(afreq2)
summary(afreq2)


# check
all(afreq1 == afreq2)


################################################################
# check -- variant splits

seqParallel(cl, f, FUN = function(gdsfile) {
		v <- seqGetFilter(gdsfile)
		sum(v$variant.sel)
	}, split = "by.variant")
# [1] 674 674


################################################################

stopCluster(cl)

# close the GDS file
seqClose(f)