correct code: childseg<-0 x:=sumchild <-0 span<-rle(x)$lengths[rle(x)$values==TRUE childseg[x]<-rep(seq_along(span), times = span) childseg[childseg == 0]<-''
On Thu, Jan 1, 2015 at 1:56 AM, Kate Ignatius <kate.ignat...@gmail.com> wrote: > Is it possible to add the following code or similar in data.table: > > childseg<-0 > x:=sumchild <-0 > span<-rle(x)$lengths[rle(x)$values==TRUE > childseg[x]<-rep(seq_along(span), times = spanLOH) > childseg[childseg == 0]<-'' > > I was hoping to do this code by SNPEFF_GENE_NAME for mum, dad and > child. The problem I'm having is with the > span<-rle(x)$lengths[rle(x)$values==TRUE line which I'm not sure can > be added to data.table. > > > On Wed, Dec 31, 2014 at 3:45 AM, Jeff Newmiller > <jdnew...@dcn.davis.ca.us> wrote: >> I do not understand the value of using the rle function in your description, >> but the code below appears to produce the table you want. >> >> Note that better support for the data.table package might be found at >> stackexchange as the documentation specifies. >> >> x <- read.table( text= >> "Dad Mum Child Group >> AA RR RA A >> AA RR RR A >> AA AA AA B >> AA AA AA B >> RA AA RR B >> RR AA RR B >> AA AA AA B >> AA AA RA C >> AA AA RA C >> AA RR RA C >> ", header=TRUE, stringsAsFactors=FALSE ) >> >> library(data.table) >> DT <- data.table( x ) >> DT[ , cdad := as.integer( Dad %in% c( "AA", "RR" ) ) ] >> DT[ , sumdad := 0L ] >> DT[ 1==DT$cdad, sumdad := sum( cdad ), by=Group ] >> DT[ , cdad := NULL ] >> DT[ , cmum := as.integer( Mum %in% c( "AA", "RR" ) ) ] >> DT[ , summum := 0L ] >> DT[ 1==DT$cmum, summum := sum( cmum ), by=Group ] >> DT[ , cmum := NULL ] >> DT[ , cchild := as.integer( Child %in% c( "AA", "RR" ) ) ] >> DT[ , sumchild := 0L ] >> DT[ 1==DT$cchild, sumchild := sum( cchild ), by=Group ] >> DT[ , cchild := NULL ] >> >>> DT >> >> Dad Mum Child Group sumdad summum sumchild >> 1: AA RR RA A 2 2 0 >> 2: AA RR RR A 2 2 1 >> 3: AA AA AA B 4 5 5 >> 4: AA AA AA B 4 5 5 >> 5: RA AA RR B 0 5 5 >> 6: RR AA RR B 4 5 5 >> 7: AA AA AA B 4 5 5 >> 8: AA AA RA C 3 3 0 >> 9: AA AA RA C 3 3 0 >> 10: AA RR RA C 3 3 0 >> >> >> On Tue, 30 Dec 2014, Kate Ignatius wrote: >> >>> I'm trying to use both these packages and wondering whether they are >>> possible... >>> >>> To make this simple, my ultimate goal is determine long stretches of >>> 1s, but I want to do this within groups (hence using the data.table as >>> I use the "set key" option. However, I'm I'm not having much luck >>> making this possible. >>> >>> For example, for simplistic sake, I have the following data: >>> >>> Dad Mum Child Group >>> AA RR RA A >>> AA RR RR A >>> AA AA AA B >>> AA AA AA B >>> RA AA RR B >>> RR AA RR B >>> AA AA AA B >>> AA AA RA C >>> AA AA RA C >>> AA RR RA C >>> >>> And the following code which I know works >>> >>> hetdad <- as.numeric(x[c(1)]=="AA" | x[c(1)]=="RR") >>> sumdad <- rle(hetdad)$lengths[rle(hetdad)$values==1] >>> >>> hetmum <- as.numeric(x[c(2)]=="AA" | x[c(2)]=="RR") >>> summum <- rle(hetmum)$lengths[rle(hetmum)$values==1] >>> >>> hetchild <- as.numeric(x[c(3)]=="AA" | x[c(3)]=="RR") >>> sumchild <- rle(hetchild)$lengths[rle(hetchild)$values==1] >>> >>> However, I wish to do the above code by Group (though this file is >>> millions of rows long and groups will be larger but just wanted to >>> simply the example). >>> >>> I did something like this but of course I got an error: >>> >>> LOH[,hetdad:=as.numeric(x[c(1)]=="AA" | x[c(1)]=="RR")] >>> LOH[,sumdad:=rle(hetdad)$lengths[rle(hetdad)$values==1],by=Group] >>> LOH[,hetmum:=as.numeric(x[c(2)]=="AA" | x[c(2)]=="RR")] >>> LOH[,summum:=rle(hetmum)$lengths[rle(hetmum)$values==1],by=Group] >>> LOH[,hetchild:=as.numeric(x[c(3)]=="AA" | x[c(3)]=="RR")] >>> LOH[,sumchild:=rle(hetchild)$lengths[rle(hetchild)$values==1],by=Group] >>> >>> The reason being as I want to eventually have something like this: >>> >>> Dad Mum Child Group sumdad summum sumchild >>> AA RR RA A 2 2 0 >>> AA RR RR A 2 2 1 >>> AA AA AA B 4 5 5 >>> AA AA AA B 4 5 5 >>> RA AA RR B 0 5 5 >>> RR AA RR B 4 5 5 >>> AA AA AA B 4 5 5 >>> AA AA RA C 3 3 0 >>> AA AA RA C 3 3 0 >>> AA RR RA C 3 3 0 >>> >>> That is, I would like to have the specific counts next to what I'm >>> consecutively counting per group. So for Group A for dad there are 2 >>> AAs, there are two RRs for mum but only 1 AA or RR for the child and >>> that is RR (so the 1 is next to the RR and not the RA). >>> >>> Can this be done? >>> >>> K. >>> >>> ______________________________________________ >>> R-help@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. >>> >> >> --------------------------------------------------------------------------- >> Jeff Newmiller The ..... ..... Go Live... >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... >> Live: OO#.. Dead: OO#.. Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k >> --------------------------------------------------------------------------- ______________________________________________ R-help@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.
