SNP2GENE genome-wide plots: QQ plots and lambda parameter

Oscar Coltell Simón

unread,

Dec 1, 2021, 1:37:48 PM12/1/21

to FUMA GWAS users

Hello Kyoko:

FUMA results are very valuable for my research, but I need more data that I not able to find in any of outputs, both graphic and data files. One of the cases is getting the lambda parameter from both, the QQ plot (GWAS summary statisics) (Additional minor note: "statisics" should be corrected to "statistics") and the QQ plot (gene-based test).

In the next update, lambda could be displayed as a legend in the figure or included in the top text before the caption.

Please, could you explain to me where I can find this parameter or how to generate it from the FUMA results.

Thank you very much.

d.p.wi...@vu.nl

unread,

Dec 14, 2021, 4:29:18 AM12/14/21

to FUMA GWAS users

Hello,

Thank you for the suggestion, I will add it to the list for the next updates.

Cheers,

Doug

Arthemon Nguweneza

unread,

Sep 20, 2022, 3:53:03 AM9/20/22

to FUMA GWAS users

Hello Doug,

Do you now where I can find lambda for the QQ plots?

Thank you,

Arthemon

Marijn Schipper

unread,

Sep 21, 2022, 8:33:20 AM9/21/22

to FUMA GWAS users

Hi Arthemon,

Currently this is not implemented in FUMA.
Calculation of the lambda can be done by by running the following snippit of code in R for example:

chisq <- qchisq(1-a$P, 1)
lambda = median(chisq)/qchisq(0.5,1)
lambda

Where a$P is the p-value column of a dataframe containing your sumstats.

Cheers,

Marijn

Op dinsdag 20 september 2022 om 09:53:03 UTC+2 schreef Arthemon Nguweneza:

Reply all

Reply to author

Forward