The genotyping data are protected. We are therefore using a synthetic dataset emulating the real data. The expression and replicated genotyping data are in data/replicated_data.RData. The ready-to-use data with simulated genetic associations are in data/prepared_data.RData.
The file data/prepared_data.RData is obtained by updating the real expression data to simulate genetic associations between the synthetic genotyping data and the transcript levels. This last step is obtained by running the R file scripts/prepare_data.R after installing the R package echoseq:
if(!require(remotes)) install.packages("remotes")
remotes::install_github("hruffieux/echoseq")The package atlasqtl used for the analysis may also be installed with:
if(!require(remotes)) install.packages("remotes")
remotes::install_github("hruffieux/atlasqtl")The eQTL analysis can be run using the Rmarkdown script: scripts/atlasqtl_software_corner.Rmd. This file also acts as a simple tutorial for the use of atlasqtl.
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