I want do this work in R or Linux:
I have a matrix in text format. In this table the rows are contain SNP and columns are contain samples and between these there are genotypes and unmeasured data (A/A,C/T,0/0). Now I want to find variants that are called in 20% of the samples (that is: finding genotypes that observed in 20% of samples in each rows (for each SNP) exceould you please help me?
A B C D
1:14773 0/0 0/0 0/0 0/0
1:14907 A/G A/G A/A A/C
1:14930 A/G A/T A/G A/G
1:14933 G/A 0/0 0/0 G/A
1:14948 0/0 0/0 0/0 0/0
A clarification, is, for example, 1:14907 with A=A/Gm B=A/G, C=A/A and D=A/C a variant and you want to look for if there are 20% or more rows with this, or do you want to check all rows with, for example, A=A/G in 20% or more rows? Can you provide an example of whay exactly you want to do.
I want to calculate MAF for each row (except 0/0) and after that select rows with MAF>20%.
That is: How can I calculate MAF(minor allele frequency )for each row "except 0/0 ;that is not consider 0/0") and after that select rows with MAF>20%?
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