[R] data.table/ifelse conditional new variable question

[Kate Ignatius]

Actually - I didn't check this before, but these are not all nuclear
families (as I assumed they were).  That is, some don't have a father
or don't have a mother.... Usually if this is the case PID or MID will
become 0, respectively, for the child.  How can the code be edit to
account for this?

On Sat, Aug 16, 2014 at 8:02 PM, Kate Ignatius <kate.ignatius at gmail.com> wrote:
> 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$Sample.ID[father] :
>   replacement has length zero
>
>
>
> On Sat, Aug 16, 2014 at 6:48 PM, Jorge I Velez <jorgeivanvelez at gmail.com> wrote:
>> Dear Kate,
>>
>> Assuming you have nuclear families, one option would be:
>>
>> x <- read.table(textConnection("Family.ID Sample.ID Relationship
>> 14           62  sibling
>> 14          94  father
>> 14           63  sibling
>> 14           59 mother
>> 17         6004  father
>> 17           6003 mother
>> 17         6005   sibling
>> 17         368   sibling
>> 130           202 mother
>> 130           203  father
>> 130           204   sibling
>> 130           205   sibling
>> 130           206   sibling
>> 222         9 mother
>> 222         45  sibling
>> 222         34  sibling
>> 222         10  sibling
>> 222         11  sibling
>> 222         18  father"), header = TRUE)
>> closeAllConnections()
>>
>> xs <- with(x, split(x, Family.ID))
>> res <- do.call(rbind, lapply(xs, function(l){
>> l$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.ignatius at 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 at 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.
>>
>>