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green-striped-gecko / dartR

Importing and Analysing DArT type snp and silicodart data
GNU General Public License v3.0
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Multitest correction in HWE filter? #648

Closed DaniEstevezBarcia closed 11 months ago

DaniEstevezBarcia commented 11 months ago

Hello,

Congrats for a very fun and nice package. I wanted to check out how well the package can filter out loci out of HWE, I wanted to ask if you had incorporated any multitest correction in the analyses.

Thank you

biomatix commented 11 months ago

Hi Daniel,

If you mean is there an option for correcting for multiple comparisons, then yes.

mult.comp.adj

Whether to adjust p-values for multiple comparisons [default FALSE]. mult.comp.adj.method

Method to adjust p-values for multiple comparisons: 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr' (see details) [default 'fdr'].

Refer to ?gl.filter.hwe

Arthur

On Thu, 5 Oct 2023 at 00:25, Daniel Estévez-Barcia @.***> wrote:

Hello,

Congrats for a very fun and nice package. I wanted to check out how well the package can filter out loci out of HWE, I wanted to ask if you had incorporated any multitest correction in the analyses.

Thank you

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DaniEstevezBarcia commented 11 months ago

Thanks Arthur