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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Question about LD file #1

Closed andronekomimi closed 7 years ago

andronekomimi commented 8 years ago

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 commented 8 years ago

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/gkichaev/PAINTOR_V3.0/issues/1, or mute the thread https://github.com/notifications/unsubscribe/AE-bO5ekHFy1aNr4tYxYijzPCg4p1WpUks5qMYtMgaJpZM4I3ofL .

andronekomimi commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

Hi,

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

Thanks Audrey