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BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
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gwas.pvalue #12

Closed Tigeeeeer closed 2 years ago

Tigeeeeer commented 3 years ago

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)? out

Appreciate your help in advance!

Tigeeeeer commented 3 years ago
hewm2008 commented 3 years ago

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.