Entering edit mode
20 months ago
rheab1230
▴
140
Hello everyone, I have a genotype file.
![dput(gt_df\[1:5,1:5\])
structure(list(`GTEX-1117F` = c(0L, 0L, 0L, 1L, 0L), `GTEX-111FC` = c(0L,
0L, 0L, 2L, 0L), `GTEX-1128S` = c(0L, 0L, 0L, 2L, 0L), `GTEX-117XS` = c(0L,
0L, 0L, 1L, 0L), `GTEX-1192X` = c(0L, 0L, 0L, 1L, 0L)), row.names = c("22_20000222_C_T_b38",
"22_20000320_A_C_b38", "22_20000538_C_T_b38", "22_20000722_G_A_b38",
"22_20001035_C_T_b38"), class = "data.frame")][1]
I want to calculate minor allele frequency for each snp(eg: 22_20000222_C_T_b38 ) across the samples. So basically for this SNP: 22_20000222_C_T_b38 I want to calculate its maf across all the 205 samples. Is there any way or formula to do it. Thank you.