gwas.pvalue
Tigeeeeer opened this issue · 2 comments
Hi,
Thanks for this amazing and convenient tool,
I would like to ask one questions:
why the y axis label is -lg(Pvalue) rather than -log(Pvalue)?
Appreciate your help in advance!
Dear @Tigeeeeer
A . the Y axis [-lg(Pvalue)] is the same with [-log(Pvalue) ], some one ask me to default is to lg ,also you can use this
perl LDBlockShow-1.40/bin/ShowLDSVG -InYName "-log(Pvalue)" ...
B the file [ gwas.pvalue ] is the result of others tools , most gaws software used the diploid calculation.
C For whole chromosome LDheatmap ?
The maximum number of SNPs recommended by the software is about 10,000. It is recommended to pick out 5k-1w SNPs of the whole chromosome genome according to sliding windows.
also set this Para [-NoShowLDist] at the chr length.