Improving GWAS resolution using local score.

We used the Local Score approach to improve the resolution of GWAS and detect minor QTL.
Added by Maria Ines Fariello Rico over 3 years ago

Quantitative trait loci (QTL) with small effects, which are pervasive in quantitative phenotypic variation, are difficult to detect in genome-wide association studies (GWAS). To improve their detection, we propose to use a local score approach that accounts for the surrounding signal due to linkage disequilibrium, by accumulating association signals from contiguous single markers.

We also updated the scripts, so now is possible to compute the distribution of the local score for xi= 3 and 4, under the assumption that the p-values follow a uniform distribution.

Reference:

scorelocalfunctions.R - Functions used for computing local score with updated xi values: 3 and 4 (7.65 KB) Maria Ines Fariello Rico, 06/06/2019 12:32 AM

localscore_uniform.R - Script used to compute the local score and find significative regions (1.5 KB) Maria Ines Fariello Rico, 06/06/2019 12:32 AM

example_data_file.txt.zip - Toy example data (46.2 MB) Maria Ines Fariello Rico, 06/06/2019 12:35 AM


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