Thanks!
I think I know what is being done here but not sure how to fix the
following error:
Error in l$PID[l$\Relationship == "sibling"] <- l$Sample.ID[father] :
replacement has length zero
On Sat, Aug 16, 2014 at 6:48 PM, Jorge I Velez <jorgeivanve...@gmail.com> wrote:
> Dear Kate,
>
> Assuming you have nuclear families, one option would be:
>
> x <- read.table(textConnection("Family.ID Sample.ID Relationship
> 14 62 sibling
> 14 94 father
> 14 63 sibling
> 14 59 mother
> 17 6004 father
> 17 6003 mother
> 17 6005 sibling
> 17 368 sibling
> 130 202 mother
> 130 203 father
> 130 204 sibling
> 130 205 sibling
> 130 206 sibling
> 222 9 mother
> 222 45 sibling
> 222 34 sibling
> 222 10 sibling
> 222 11 sibling
> 222 18 father"), header = TRUE)
> closeAllConnections()
>
> xs <- with(x, split(x, Family.ID))
> res <- do.call(rbind, lapply(xs, function(l){
> l$PID <- l$MID <- 0
> father <- with(l, Relationship == 'father')
> mother <- with(l, Relationship == 'mother')
> l$PID[l$Relationship == 'sibling'] <- l$Sample.ID[father]
> l$MID[l$Relationship == 'sibling'] <- l$Sample.ID[mother]
> l
> }))
> res
>
> HTH,
> Jorge.-
>
>
> Best regards,
> Jorge.-
>
>
>
> On Sun, Aug 17, 2014 at 5:42 AM, Kate Ignatius <kate.ignat...@gmail.com>
> wrote:
>>
>> Hi,
>>
>> I have a data.table question (as well as if else statement query).
>>
>> I have a large list of families (file has 935 individuals that are
>> sorted by famiy of varying sizes). At the moment the file has the
>> columns:
>>
>> SampleID FamilyID Relationship
>>
>> To prevent from having to make a pedigree file by hand - ie adding a
>> PaternalID and a MaternalID one by one I want to try write a script
>> that will quickly do this for me (I eventually want to run this
>> through a program such as plink) Is there a way to use data.table
>> (maybe in conjucntion with ifelse to do this effectively)?
>>
>> An example of the file is something like:
>>
>> Family.ID Sample.ID Relationship
>> 14 62 sibling
>> 14 94 father
>> 14 63 sibling
>> 14 59 mother
>> 17 6004 father
>> 17 6003 mother
>> 17 6005 sibling
>> 17 368 sibling
>> 130 202 mother
>> 130 203 father
>> 130 204 sibling
>> 130 205 sibling
>> 130 206 sibling
>> 222 9 mother
>> 222 45 sibling
>> 222 34 sibling
>> 222 10 sibling
>> 222 11 sibling
>> 222 18 father
>>
>> But the goal is to have a file like this:
>>
>> Family.ID Sample.ID Relationship PID MID
>> 14 62 sibling 94 59
>> 14 94 father 0 0
>> 14 63 sibling 94 59
>> 14 59 mother 0 0
>> 17 6004 father 0 0
>> 17 6003 mother 0 0
>> 17 6005 sibling 6004 6003
>> 17 368 sibling 6004 6003
>> 130 202 mother 0 0
>> 130 203 father 0 0
>> 130 204 sibling 203 202
>> 130 205 sibling 203 202
>> 130 206 sibling 203 202
>> 222 9 mother 0 0
>> 222 45 sibling 18 9
>> 222 34 sibling 18 9
>> 222 10 sibling 18 9
>> 222 11 sibling 18 9
>> 222 18 father 0 0
>>
>> I've tried searches for this but with no luck. Greatly appreciate any
>> help - even if its just a link to a great example/solution!
>>
>> Thanks!
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> 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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