[R] how to turn column into column names and fill it with values

[Ana Marija]

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.4567 using 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.anamarija using 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
>>
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