[R] making code (loop) more efficient
Ana Marija
@okov|c@@n@m@r|j@ @end|ng |rom gm@||@com
Wed Dec 16 03:44:57 CET 2020
Hi Jim,
as always you're completely right, this is what is happening:
> head(a)
top1 blup lasso enet
rs4980905:184404:C:A 0.07692622 -1.881795e-04 0 0
rs7978751:187541:G:C 0.62411425 9.934994e-04 0 0
rs2368831:188285:C:T 0.69529158 1.211028e-03 0 0
rs12830904:188335:T:A 0.92793158 -9.143555e-05 0 0
rs1500098:189093:G:C 0.42032471 9.001814e-04 0 0
rs79410690:190097:G:A 0.26194244 5.019037e-04 0 0
> names <- rownames(a)
> data <- data.table(names, a["blup"])
> head(data)
names V2
1: rs4980905:184404:C:A NA
2: rs7978751:187541:G:C NA
3: rs2368831:188285:C:T NA
4: rs12830904:188335:T:A NA
5: rs1500098:189093:G:C NA
6: rs79410690:190097:G:A NA
So my goal is to transform what is in "a" to this for every RDat file:
rsid weight ref_allele eff_allele
1: rs72763981 9.376766e-09 C G
2: rs144383755 -2.093346e-09 A G
3: rs1925717 1.511376e-08 T C
4: rs61827307 -1.625302e-08 C A
5: rs61827308 -1.625302e-08 G C
6: rs199623136 -9.128354e-10 GC G
WGT
1: retina.ENSG00000135776.wgt.RDat
2: retina.ENSG00000135776.wgt.RDat
3: retina.ENSG00000135776.wgt.RDat
4: retina.ENSG00000135776.wgt.RDat
5: retina.ENSG00000135776.wgt.RDat
6: retina.ENSG00000135776.wgt.RDat
so from rs4980905:184404:C:A I would take rs4980905 to be in column
"rsid", C in column "ref_allele" and A to be in column "eff_allele",
WGT column would just be filled with a name of the particular RDat
file.
So the issue is in these lines:
a <- get(load(files[i]))
names <- rownames(a)
data <- data.table(names, a["blup"])
nm1 <- c("rsid", "ref_allele", "eff_allele")
any idea how I can rewrite this?
On Tue, Dec 15, 2020 at 8:30 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> Hi Ana,
> I would look at "data" in your second example and see if it contains a
> column named "blup" or just the values that were extracted from
> a$blup. Also, I assume that weight=blup looks for an object named
> "blup", which may not be there.
>
> Jim
>
> On Wed, Dec 16, 2020 at 1:20 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >
> > Hi Jim,
> >
> > Maybe my post is confusing.
> >
> > so "dd" came from my slow code and I don't use it again in parallelized code.
> >
> > So for example for one of my files:
> >
> > if
> > i="retina.ENSG00000120647.wgt.RDat"
> > > a <- get(load(i))
> > > head(a)
> > top1 blup lasso enet
> > rs4980905:184404:C:A 0.07692622 -1.881795e-04 0 0
> > rs7978751:187541:G:C 0.62411425 9.934994e-04 0 0
> > rs2368831:188285:C:T 0.69529158 1.211028e-03 0 0
> > ...
> >
> > Slow code was posted just to show what was running very slow and it
> > was running. I really need help fixing parallelized version.
> >
> > On Tue, Dec 15, 2020 at 7:35 PM Jim Lemon <drjimlemon using gmail.com> wrote:
> > >
> > > Hi Ana,
> > > My guess is that in your second code fragment you are assigning the
> > > rownames of "a" and the _values_ contained in a$blup to the data.table
> > > "data". As I don't have much experience with data tables I may be
> > > wrong, but I suspect that the column name "blup" may not be visible or
> > > even present in "data". I don't see it in "dd" above this code
> > > fragment.
> > >
> > > Jim
> > >
> > > On Wed, Dec 16, 2020 at 11:12 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> > > >
> > > > Hello,
> > > >
> > > > I made a terribly inefficient code which runs forever but it does run.
> > > >
> > > > library(dplyr)
> > > > library(splitstackshape)
> > > >
> > > > datalist = list()
> > > > files <- list.files("/WEIGHTS1/Retina", pattern=".RDat", ignore.case=T)
> > > >
> > > > for(i in files)
> > > > {
> > > > a<-get(load(i))
> > > > names <- rownames(a)
> > > > data <- as.data.frame(cbind(names,a))
> > > > rownames(data) <- NULL
> > > > dd=na.omit(concat.split.multiple(data = data, split.cols = c("names"),
> > > > seps = ":"))
> > > > dd=select(dd,names_1,blup,names_3,names_4)
> > > > colnames(dd)=c("rsid","weight","ref_allele","eff_allele")
> > > > dd$WGT<-i
> > > > datalist[[i]] <- dd # add it to your list
> > > > }
> > > >
> > > > big_data = do.call(rbind, datalist)
> > > >
> > > > There is 17345 RDat files this loop has to go through. And each file
> > > > has approximately 10,000 lines. All RDat files can be downloaded from
> > > > here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115828 and
> > > > they are compressed in this file: GSE115828_retina_TWAS_wgts.tar.gz .
> > > > And subset of 3 of those .RDat files is here:
> > > > https://github.com/montenegrina/sample
> > > >
> > > > For one of those files, say i="retina.ENSG00000135776.wgt.RDat"
> > > > dd looks like this:
> > > >
> > > > > head(dd)
> > > > rsid weight ref_allele eff_allele
> > > > 1: rs72763981 9.376766e-09 C G
> > > > 2: rs144383755 -2.093346e-09 A G
> > > > 3: rs1925717 1.511376e-08 T C
> > > > 4: rs61827307 -1.625302e-08 C A
> > > > 5: rs61827308 -1.625302e-08 G C
> > > > 6: rs199623136 -9.128354e-10 GC G
> > > > WGT
> > > > 1: retina.ENSG00000135776.wgt.RDat
> > > > 2: retina.ENSG00000135776.wgt.RDat
> > > > 3: retina.ENSG00000135776.wgt.RDat
> > > > 4: retina.ENSG00000135776.wgt.RDat
> > > > 5: retina.ENSG00000135776.wgt.RDat
> > > > 6: retina.ENSG00000135776.wgt.RDat
> > > >
> > > > so on attempt to parallelize this I did this:
> > > >
> > > > library(parallel)
> > > > library(data.table)
> > > > library(foreach)
> > > > library(doSNOW)
> > > >
> > > > n <- parallel::detectCores()
> > > > cl <- parallel::makeCluster(n, type = "SOCK")
> > > > doSNOW::registerDoSNOW(cl)
> > > > files <- list.files("/WEIGHTS1/Retina", pattern=".RDat", ignore.case=T)
> > > >
> > > > lst_out <- foreach::foreach(i = seq_along(files),
> > > > .packages = c("data.table") ) %dopar% {
> > > >
> > > > a <- get(load(files[i]))
> > > > names <- rownames(a)
> > > > data <- data.table(names, a["blup"])
> > > > nm1 <- c("rsid", "ref_allele", "eff_allele")
> > > > data[, (nm1) := tstrsplit(names, ":")[-2]]
> > > > return(data[, .(rsid, weight = blup, ref_allele, eff_allele)][,
> > > > WGT := files[i]][])
> > > > }
> > > > parallel::stopCluster(cl)
> > > >
> > > > big_data <- rbindlist(lst_out)
> > > >
> > > > I am getting this Error:
> > > >
> > > > Error in { : task 7 failed - "object 'blup' not found"
> > > > > parallel::stopCluster(cl)
> > > >
> > > > Can you please advise,
> > > > Ana
> > > >
> > > > ______________________________________________
> > > > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > > > and provide commented, minimal, self-contained, reproducible code.
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