README.md
In liangyy/finemapAim: Wrapper for AIM
run-aim
Run AIM here.
Here we wrap it up as an R function taking genotype, ASC data, eQTL results and returning the PIP and CS.
I mostly follow the paper "Methods" section "Application to GTEx data" but instead of using CAVIAR as fine-mapping solver we deploy susieR since it is much faster when we include all SNPs in the cis-window (thousands of SNPs).
I use both of the meta-analysis scheme S^M1 and S^M2 as suggested by the paper.
And we report the results of the scheme with smaller CS size on average.
Note
It relies on the current screen shot of susieR (610b5bb754e9c9f970eef15a5a194fb9dc421caa).
It matters since it relies on susieR::susie_rss.
liangyy/finemapAim documentation built on Sept. 4, 2020, 9:51 p.m.
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run-aim
Run AIM here.
Here we wrap it up as an R function taking genotype, ASC data, eQTL results and returning the PIP and CS. I mostly follow the paper "Methods" section "Application to GTEx data" but instead of using CAVIAR as fine-mapping solver we deploy susieR since it is much faster when we include all SNPs in the cis-window (thousands of SNPs). I use both of the meta-analysis scheme S^M1 and S^M2 as suggested by the paper. And we report the results of the scheme with smaller CS size on average.
Note
It relies on the current screen shot of susieR (610b5bb754e9c9f970eef15a5a194fb9dc421caa).
It matters since it relies on susieR::susie_rss.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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