Question: (Closed) recoding genotype in R
0
Fersal • 20 wrote:
I am trying to re-code the following genotype data frame from biallelic code to "A", "B" code. corresponding to P1 and P2, respectively, which in turns correspond to the two parents. Please consider the following example.
SNP P1 P2 in1 in2 in3 in4
M01 CC GG CC GG CC GG
M02 TT CC TT TT CC TT
M03 AA GG AA GG GG GG
M04 CC GG CC GG CC GG
M05 GG AA AA GG AA AA
M06 CC GG CC GG CC CC
So that all the individuals that have the same genotype of P1 would be "A" and the ones that carries the genotype from P2 would be "B". Like the following table:
SNP P1 P2 in1 in2 in3 in4
M01 CC GG A B A B
M02 TT CC A A B A
M03 AA GG A B B B
M04 CC GG A B A B
M05 GG AA B B B B
M06 CC GG A B A A
I have tried the following code in R
df[is.na(df[4:7]) == as.character(df$P1)] = "A"
df[is.na(df[4:7]) == as.character(df$P2)] = "B"
Error in `[<-.data.frame`(`*tmp*`, is.na(df[4:7]) == as.character(df$P1), :
unsupported matrix index in replacement
Any idea how to solve it?
Hello Fersal!
We believe that this post does not fit the main topic of this site.
This is an R question and has nothing to do with the data involved. Please read up on how to index 2 dimensional objects in R
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!