Name: mayoeQTL
Owner: Sage Bionetworks
Description: null
Created: 2015-03-02 23:29:50.0
Updated: 2015-03-10 01:13:00.0
Pushed: 2015-03-03 21:18:34.0
Homepage: null
Size: 152
Language: R
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Script to download MayoLOAD GWAS genotypes, MayoEGWAS gene expression data, and covariates for each data-set
In addition, this script synchronizes the sample ids between all the data frames so that they are standard
Author: Benjamin A Logsdon (ben.logsdon@sagebase.org)
Synapse R client installed (https://www.synapse.org/#!Synapse:syn1834618)
Have a synapse account (https://www.synapse.org/#!RegisterAccount:0)
Have plink installed (http://pngu.mgh.harvard.edu/~purcell/plink/)
Data access approval to MayoLOADGWAS data (https://www.synapse.org/#!Synapse:syn2954402)
Data access approval to MayoEGWAS data (https://www.synapse.org/#!Synapse:syn2910255)
Unix like shell environment
clone repo into a local directory
git clone https://github.com/blogsdon/mayoeQTL.git
run script
./grabMayoEGWASdata.sh
After script is run, all data will be downloaded into your local directory into MayoEGWASAnalyses/. You can now open an R session in the newly created MayoEGWASAnalyses directory, and then source the loadEGWASdata.R script. This will load the expression data, covariate data, and chromosome 22 for the cerebellum samples into the R session.
cd MayoEGWASanalyses/
R
source('../loadEGWASdata.R')
Once these scripts are run the data is stored in R as follows.
cere_cov contains the covariates for the cerebellum gene expression data
gwas_cere_cov contains the covariates for the genotype data for the cerebellum samples
mayo_egwas_cere_data contains the expression data for the cerebellum samples
mayo_geno_cere_22 contains the genotype data for the 22nd chromosome for the cerebellum samples
tcx_cov contains the covariates for the temporal cortex expression data
gwas_tcx_cov contains the genotype covariates for the temporal cortex samples
mayo_egwas_tcx_data conatins the expression data for the temporal cortex samples
reorderGenotypes function can be used to synchronize additional genotype data that can be read in from MayoEGWASanalyses/cerebellumGenotypes or MayoEGWASanalyses/temporalCortexGenotypes as shown in the loadEGWASdata.R script.