Question

Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file

0

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Vinicius Henrique da Silva ▴ 40

@vinicius-henrique-da-silva-6713

Last seen 21 months ago

Brazil

There is a function to obtain a data-frame containing the SNP tag and the correspondent Minimum allele frequency (MAF) from Genomic Data Structure (GDS) file?

I tried to find a function in SNPRelate and GWASTools packages, but I did not find what I was looking for. I will be grateful for any light here.

snprelate GWASTools • 1.0k views

ADD COMMENT • link updated 5.7 years ago by Adrienne Stilp ▴ 30 • written 5.7 years ago by Vinicius Henrique da Silva ▴ 40

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Adrienne Stilp ▴ 30

@adrienne-stilp-6412

Last seen 2.3 years ago

United States

You can use the alleleFrequency function in GWASTools for array data or the alleleFrequency function in SeqVarTools for sequencing data.

ADD COMMENT • link 5.7 years ago Adrienne Stilp ▴ 30

score 2 · Accepted Answer · 2016-05-25

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James W. MacDonald 58k

@james-w-macdonald-5106

Last seen 5 hours ago

United States

Did you look at ?snpgdsSNPRateFreq in the SNPRelate package?

ADD COMMENT • link 5.7 years ago James W. MacDonald 58k