calculating MAF (Minor Allele Frequency) and missing rate
Data contains a .csv file with marker names in the A column and their genotype data for each marker in the rest of the columns. that is "ng_rice_snp" This data is filtered and cleaned to calculate missing rate and minor allele frequency. 0 - homozygous reference allele 1 - heterozygous allele 2 - homozygous alternative allele. "-" = missing rate I first calculated the missing rate for each marker (row) for all the individual samples. later created a function called "calculate_maf" to calculate the number of reference alleles and the number of alternative alleles from, 0,1,2 later calculated the ref and alt frequencies within this function.
using the "apply" function in R.studio I have applied this function over all the markers to calculate MAF. with the write.csv function, I have updated a new .csv file with the missing rate and MAF(minor allele frequency) for all the markers.
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