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Fig. 4 | BioData Mining

Fig. 4

From: eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals

Fig. 4

Example eQTpLot for LDL cholesterol and the gene BBS1, discriminating between congruous and incongruous variants. eQTpLot was used to generate a series of plots illustrating the colocalization between eQTLs for the gene BBS1 and a GWAS signal for the LDL cholesterol trait on chromosome 11 as described in example 3, with an analysis identical to that described for Fig. 3, but with the additional discrimination between variants with congruous and incongruous directions of effect. Panel A is generated identically to panel 1A and 3A, only instead of using a single color scale, variants with congruous effects are plotted using a blue color scale, while variants with incongruous effects are plotted using a red color scale. Panels B-D are identical to panels 3B-D. Panel E and F both represent P-P plots, generated similarly to the P-P plot in panel 3E. For panel E, however, the analysis is confined only to variants with congruous directions of effect, while for panel F the analysis includes only variants with incongruous directions of effect. A lead variant is indicated in both panels E anf F, and both are also labeled in panel A

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