[R] data.table/ifelse conditional new variable question
Kate Ignatius
kate.ignatius at gmail.com
Sun Aug 17 03:47:41 CEST 2014
Yep - you're right - missing parents are indicated as zero in the M/PID field.
The above code worked with a few errors:
1: In l$PID[l$Relationship == "sibling"] <- l$Sample.ID[father] :
number of items to replace is not a multiple of replacement length
2: In l$PID[l$Relationship == "sibling"] <- l$Sample.ID[father] :
number of items to replace is not a multiple of replacement length
3: In l$PID[l$Relationship == "sibling"] <- l$Sample.ID[father] :
number of items to replace is not a multiple of replacement length
4: In l$MID[l$Relationship == "sibling"] <- l$Sample.ID[mother] :
number of items to replace is not a multiple of replacement length
looking at the output I get numbers where the father/mother ID should
be in the M/PID field. For example:
2702 349 mother 0 0
2702 3456 sibling 0 842
2702 9980 sibling 0 842
3064 3 father 0 0
3064 4 mother 0 0
3064 5 sibling 879 880
3064 86 sibling 879 880
3064 87 sibling 879 880
On Sat, Aug 16, 2014 at 9:31 PM, Jorge I Velez <jorgeivanvelez at gmail.com> wrote:
> Dear Kate,
>
> Try this:
>
> res <- do.call(rbind, lapply(xs, function(l){
> l$PID <- l$MID <- 0
> father <- with(l, Relationship == 'father')
> mother <- with(l, Relationship == 'mother')
> if(sum(father) == 0)
> l$PID[l$Relationship == 'sibling'] <- 0
> else l$PID[l$Relationship == 'sibling'] <- l$Sample.ID[father]
> if(sum(mother) == 0)
> l$MID[l$Relationship == 'sibling'] <- 0
> else l$MID[l$Relationship == 'sibling'] <- l$Sample.ID[mother]
> l
> }))
>
> It is assumed that when either parent is not available the M/PID is 0.
>
> Best,
> Jorge.-
>
>
> On Sun, Aug 17, 2014 at 10:58 AM, Kate Ignatius <kate.ignatius at gmail.com>
> wrote:
>>
>> 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.
>> >>
>> >>
>
>
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