R - Count number of Samples with mutation per gene
Hey,
I have an annotated VCF file in R. So basically one column with the gene name and multiple columns with the genotype (0,1,2, = WT, HET, HOM). Now I would like to summarize the number of how many individual samples have one or more mutation per gene. Any ideas on how to do that ?
Thanks!
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Nicola Casiraghi
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jan.haas •
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jan.haas •
1 answer
you can apply the function table() for each row in your VCF:
> GENE1 = c(1,2,2,2,2,0,0,1,1,1)
> table(GENE1)
GENE1
0 1 2
2 4 4
thus the result is a vector with a counter for each genotype found in the considered gene.
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