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

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

0

3.5 years ago by

Vinicius Henrique da Silva • 40

Brazil

Vinicius Henrique da Silva • 40 wrote:

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.

gwastools snprelate • 713 views

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modified 3.5 years ago by Adrienne Stilp • 30 • written 3.5 years ago by Vinicius Henrique da Silva • 40

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

2

3.5 years ago by

James W. MacDonald ♦ 51k

United States

James W. MacDonald ♦ 51k wrote:

Did you look at ?snpgdsSNPRateFreq in the SNPRelate package?

ADD COMMENT • link written 3.5 years ago by James W. MacDonald ♦ 51k

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

1

3.5 years ago by

Adrienne Stilp • 30

United States

Adrienne Stilp • 30 wrote:

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

ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Adrienne Stilp • 30

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