Last updated: 2018-06-01

workflowr checks: (Click a bullet for more information)

  • ✔ R Markdown file: up-to-date

    Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

  • ✔ Repository version: 401fd65

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 
    
Ignored files:
    Ignored:    .sos/
    Ignored:    data/.sos/
    Ignored:    output/MatrixEQTLSumStats.Portable.Z.coved.K3.P3.lite.single.expanded.V1.loglik.rds
    Ignored:    workflows/.ipynb_checkpoints/
    Ignored:    workflows/.sos/

Untracked files:
    Untracked:  gtex6_workflow_output/

Unstaged changes:
    Modified:   workflows/README
    Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
Expand here to see past versions:
    File Version Author Date Message
    Rmd 401fd65 Peter Carbonetto 2018-06-01 wflow_publish(“fastqtl2mash.Rmd”)
    Rmd 6a456e6 Peter Carbonetto 2018-06-01 Moved some output files to data folder; removed some old files from

Overview

We provide code to convert association statistics in FastQTL format, or a format similar to FastQTL, to a format that is more convenient for mash analysis. Here we give instructions for using this code, and demonstrate how to convert a toy FastQTL data set. This toy data set is included in the git repository.

If you find a bug in any of these steps, please post an issue.

Converting eQTL summary statistics to MASH format

Here we explain how the MatrixEQTLSumStats.Portable.Z.rds data file was generated from the source data downloaded from the GTEx Portal. The source data are the SNP-gene association statistics from release 6 of the GTEx Project (GTEx_Analysis_V6_all-snp-gene-associations.tar).

Under the repo you will find workflows/fastqtl_to_mash.ipynb to convert eQTL summary statistics (default to fastqtl format) to MASH format. Computation is configured to run in parallel for eQTL results from multiple studies. Example data-set can be found at data/eQTLDataDemo. The workflow file is documented in itself, and has a few options to customize the input and output.

To read what’s available, run:

mash-docker sos run workflows/fastqtl_to_mash.ipynb export

and read the HTML files output/fastqtl_to_mash.lite.html and output/fastqtl_to_mash.full.html

To run the conversion:

mash-docker sos run workflows/fastqtl_to_mash.ipynb \
  --data_list data/eQTLDataDemo/FastQTLSumStats.list \
  --gene_list data/eQTLDataDemo/GTEx_genes.txt

In practice for GTEx data the conversion is computationally intensive and is best done on a cluster environment with configurations to run the workflow across different nodes.

This reproducible R Markdown analysis was created with workflowr 1.0.1.9000