[R] data.table/ifelse conditional new variable question
Kate Ignatius
kate.ignatius at gmail.com
Sun Aug 17 04:02:55 CEST 2014
Actually - your code is not wrong... because this is a large file I
went through the file to see if there was anything wrong with it -
looks like there are two fathers or three mothers in some families.
Taking these duplicates out fixed the problem.
Sorry about the confusion! And thanks so much for your help!
On Sat, Aug 16, 2014 at 9:53 PM, Jorge I Velez <jorgeivanvelez at gmail.com> wrote:
> Perhaps I am missing something but I do not get the same result:
>
> x <- read.table(textConnection("Family.ID Sample.ID Relationship
> 2702 349 mother
> 2702 3456 sibling
> 2702 9980 sibling
> 3064 3 father
> 3064 4 mother
> 3064 5 sibling
> 3064 86 sibling
> 3064 87 sibling"), 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')
> 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
> }))
> #Family.ID Sample.ID Relationship MID PID
> #2702.1 2702 349 mother 0 0
> #2702.2 2702 3456 sibling 349 0
> #2702.3 2702 9980 sibling 349 0
> #3064.4 3064 3 father 0 0
> #3064.5 3064 4 mother 0 0
> #3064.6 3064 5 sibling 4 3
> #3064.7 3064 86 sibling 4 3
> #3064.8 3064 87 sibling 4 3
>
> HTH,
> Jorge.-
>
>
>
>
> On Sun, Aug 17, 2014 at 11:47 AM, Kate Ignatius <kate.ignatius at gmail.com>
> wrote:
>>
>> 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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