2 hours ago by
United States
Dear all
good afternoon
i have example snp genotyping data like this
LOCUS POS REF ALLELE 2000 3000
MC10 713 T C NA NA
MC10 760 T C NA NA
now i want to replace MC10 with SNP1, SNP2 and so no down the file and would like to insert chr column with dummy chromosome number let 1, also would like replace A with A/A, T with T/T, G with G/G and C with C/C in both REF and ALLELE columns and also replace NA with REF column values (ex NA of 2000 column to T/T). Finally i want to concatenate LOCUS, CHR and POS columns with _ into like this SNP1_1_713. I wish to like to like have data like this
LOCUS CHR POS MAR REF ALLELE 2000 3000
SNP1 1 713 SNP1_1_713 T/T C/C T/T T/T
SNP2 1 760 SNP2_1_760 T/T C/C T/T T/T
I tried with gsub, mutate etc in tidyverse and dplyr packages and tried within function to achieve my target but unsuccessful. please find my example data here
can any one help me to get my expected results with R? anyhelp in this regard will be highly appreciated
Thanks in advance
