HI Bert,
thank you for getting back to me.
I tried this:
> dat <- cbind(mc, matrix(0,ncol = 34))
> head(dat)
FID IID PLATE 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
1 fam0110 G110 4RWG569 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 fam0113 G113 cherry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 fam0114 G114 cherry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 fam0117 G117 4RWG569 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 fam0118 G118 5XAV049 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 fam0119 G119 cherry 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
23 24 25 26 27 28 29 30 31 32 33 34
1 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0
> names(dat) <- c(names(dat)[1:34], unique(dat$PLATE))
Error in names(dat) <- c(names(dat)[1:34], unique(dat$PLATE)) :
'names' attribute [68] must be the same length as the vector [37]
so names should include FID,IID,PLATE plus unique dat$PLATE
how do I fix that so the code works?
Also I tried a bit on my own:
> head(mc)
FID IID PLATE
1 fam0110 G110 4RWG569
2 fam0113 G113 cherry
3 fam0114 G114 cherry
4 fam0117 G117 4RWG569
5 fam0118 G118 5XAV049
6 fam0119 G119 cherry
...
m2=tapply(mc$IID, list(FID=mc$FID, PLATE=mc$PLATE), mean)
m2=as.data.frame(m2)
library(data.table)
m3=setDT(m2, keep.rownames = TRUE)[]
colnames(m3)[1] <- "FID"
mt=merge(mc,m3,by="FID")
> head(mt)
FID IID PLATE 0VXC556 1CNF297 1CWO500 1DXJ626 1LTX827 1SHK635 1TNP840
1 fam0110 G110 4RWG569 NA NA NA NA NA NA NA
2 fam0113 G113 cherry NA NA NA NA NA NA NA
3 fam0114 G114 cherry NA NA NA NA NA NA NA
4 fam0117 G117 4RWG569 NA NA NA NA NA NA NA
5 fam0118 G118 5XAV049 NA NA NA NA NA NA NA
6 fam0119 G119 cherry NA NA NA NA NA NA NA
1URP242 2BKX529 2PAG415 3DEF425 3ECO791 3FQM386 3KYJ479 3XHK903 4RWG569
1 NA NA NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA NA NA
4 NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA
6 NA NA NA NA NA NA NA NA NA
...
so this gives me the correct columns. Now is the question of how to
replace NA with 2 id column name matches the rownname in PLATE column
with 2 otherwise it is 1.
Cheers,
Ana
On Tue, Sep 29, 2020 at 11:46 AM Bert Gunter <bgunter.4...@gmail.com> wrote:
>
> I am not sure reshape2 is appropriate for this task, but, assuming I
> understand correctly, it's quite easy without it. The following is one way,
> which probably can be done more elegantly and efficiently, but I think it
> does what you want.
>
> "dat" is your example data frame, in which the columns were read in with
> "stringsAsFactors" = FALSE (this is important!)
>
> dat <- cbind(dat, matrix(0,ncol = 3)) ## change 3 to 34 for your full data
> names(dat) <- c(names(dat)[1:3], unique(dat$PLATE))
> for(i in 4:ncol(dat)) dat[,i] <- 1 + (names(dat)[i]== dat$PLATE)
> dat
>
> Result:
>
> FID IID PLATE 4RWG569 cherry 5XAV049
> 1 fam0110 G110 4RWG569 2 1 1
> 2 fam0113 G113 cherry 1 2 1
> 3 fam0114 G114 cherry 1 2 1
> 4 fam0117 G117 4RWG569 2 1 1
> 5 fam0118 G118 5XAV049 1 1 2
> 6 fam0119 G119 cherry 1 2 1
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Tue, Sep 29, 2020 at 9:19 AM Ana Marija <sokovic.anamar...@gmail.com>
> wrote:
>>
>> Hello,
>>
>> I have a data frame like this:
>>
>> > head(mc)
>> FID IID PLATE
>> 1 fam0110 G110 4RWG569
>> 2 fam0113 G113 cherry
>> 3 fam0114 G114 cherry
>> 4 fam0117 G117 4RWG569
>> 5 fam0118 G118 5XAV049
>> 6 fam0119 G119 cherry
>> ...
>> > dim(mc)
>> [1] 1625 4
>> > length(unique(mc$PLATE))
>> [1] 34
>>
>> I am trying to make a new data frame which would look like this:
>> FID IID PLATE 4RWG569 cherry 5XAV049 ...
>> 1 fam0110 G110 4RWG569 2 1 1
>> 2 fam0113 G113 cherry 1 2 1
>> 3 fam0114 G114 cherry 1 2 1
>> 4 fam0117 G117 4RWG569 2 1 1
>> 5 fam0118 G118 5XAV049 2 1 1
>> 6 fam0119 G119 cherry 1 2 1
>> ...
>>
>> so the new data frame would have an additional 34 columns (for every
>> unique mc$PLATE) and if in the row of PLATE column the value is ==to
>> that column name I would have 2 otherwise 1
>>
>> I tried to do this with:
>>
>> library(reshape2)
>> > m2=dcast(mc, IID ~ PLATE)
>> Using PLATE as value column: use value.var to override.
>>
>> Please advise,
>> Ana
>>
>> ______________________________________________
>> 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.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
