Question about LD file

[andronekomimi]

Hi,

I see that your LD files (in SampleData directory) contain negative values. I was thinking that LD values was between 0 and 1. Is there a special meaning ?

Moreover, what is the best value to deal with NA value in LD files ?

Thx a lot
Audrey

[gkichaev]

Hi Audrey,

The ld matrix is composed of signed Pearson correlations not r-squared.

NA values are probably monomorphic snps. I'd recommend dropping them.
Paintor 3 does not have faculties to deal with NA anymore.

Gleb.

On Thursday, June 16, 2016, Audrey Lemaçon notifications@github.com wrote:

Hi,

I see that your LD files (in SampleData directory) contain negative
values. I was thinking that LD values was between 0 and 1. Is there a
special meaning ?

Moreover, what is the best value to deal with NA value in LD files ?

Thx a lot
Audrey

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[andronekomimi]

Hi Gleb,

Thank you for your answer.
Do you use the sign of the correlation in the program or can I use the squared root of my r-squared values as an input ?

Audrey.

[gkichaev]

Yes the sign is extremely important for the output to be valid. The
reference and alternate alleles on which the zscores are computed must also
match the Pearson correlations.

Gleb

On Friday, June 17, 2016, Audrey Lemaçon notifications@github.com wrote:

Hi Gleb,

Thank you for your answer.
Do you use the sign of the correlation in the program or can I use the
squared root of my r-squared values as an input ?

Audrey.

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[andronekomimi]

Hi,

Thanks a lot for your answer.
Do you have a favorite tool to get 1000G's Pearson correlations ?

Thanks
Audrey