Recoding HLA Alleles by 01

Question

[seymakatrinli]

I have a large data frame with HLA alleles like that:

> sample.id allele1 allele2
1   44:03   45:01
2   15:16   15:16
3   07:02   15:03
4   07:02   18:01
5   35:01   44:03

I want to convert HLA alleles in genotypes such as:

> sample.id 44:03   45:01   15:16   07:02   15:03   18:01   35:01
1   1   1   0   0   0   0   0
2   0   0   2   0   0   0   0
3   0   0   0   1   1   0   0
4   0   0   0   1   0   1   0
5   1   0   0   0   0   0   1

I have a large data frame with 5000 samples and 65 alleles. So at the end I should have a column for each sample and each allele. So dimensions should be 5000x65. Do you know any R package, tools etc for that conversion?

Thanks!

Answer 1

[Kevin Blighe]

With that many variables, you'll struggle to do it quickly in R. You could try this awk solution outside of R. It should work with any number of alleles and samples. Tested on linux (Ubuntu) BASH, but should also work on MAC.

cat HLA.tsv
sample.id   allele1 allele2
1   44:03   45:01
2   15:16   15:16
3   07:02   15:03
4   07:02   18:01
5   35:01   44:03

.

awk -F"\t" 'NR==FNR {if (NR==1) printf $1"\t"; if (NR>1) {for (i=2; i<=NF; i++) allele[$(i)]}; next} {if (FNR==1) {for (a in allele) printf a"\t"}; if (FNR>1) {printf "\n"$1"\t"; present=0; for (a in allele) {present=0; for (i=2; i<=NF; i++) {if ($(i)==a) {present=1}}; if (present==1) {printf "1\t"} else {printf "0\t"}; if (i==NF) printf "\n"}}} END {printf "\n"}' HLA.tsv HLA.tsv | sed 's/\t$//g'
sample.id   45:01   44:03   18:01   07:02   15:03   35:01   15:16
1           1       1       0       0       0       0       0
2           0       0       0       0       0       0       1
3           0       0       0       1       1       0       0
4           0       0       1       1       0       0       0
5           0       1       0       0       0       1       0

[seta]

Hi Kevin,

what about the conversion of HLA allele to popgene format; could you please take a look at this post ? do you have any suggestion?

Thanks