https://github.com/soedinglab/gxpred

Development branch of GxPRED
https://github.com/soedinglab/gxpred

Last synced: 11 months ago
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Development branch of GxPRED

• Host: GitHub
• URL: https://github.com/soedinglab/gxpred
• Owner: soedinglab
• Created: 2017-10-11T11:42:32.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-08-15T12:05:58.000Z (almost 8 years ago)
• Last Synced: 2025-02-26T14:15:56.630Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 17.3 MB
• Stars: 0
• Watchers: 6
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

          
# GxPRED #

This is the development branch of Gene Expression Prediction Algorithm, under the production name GxPRED.

### What is this repository for? ###

* Development of GxPRED

* v0.01

### How to run? ###

GxPRED provides core utilities / API for learning and predicting gene expression levels from genotype. Examples are shown in the base directory for learning from gEUVADIS data (`learn_from_geuvadis.py`) and predicting on GTEx data (`predict_on_gtex.py`). You can adapt these files for any dataset.

    CODEBASE = "/path/to/this/directory"

    TRAINVCF = "/path/to/gz/vcf/file/for/training"

    TRAINRPKM = "/path/to/normalized/gene/expression/file/for/training"

    TRAINGTF = "/path/to/gtf/file_in_gz_format"

    CHROM = "21" # change it to whichever chromosome you are interested 

    PREDVCF = "/path/to/gz/vcf/for/prediction/samples"

    MODELDIR = "/path/to/directory/where/model/will/be/saved"

    

    python ${CODEBASE}/learn_from_geuvadis.py   --vcf ${TRAINVCF} --rpkm ${TRAINRPKM} --gtf ${TRAINGTF} --chrom ${CHROM} --params 0.01 0.0 0.01 0.001 0.001 --outdir ${MODELDIR}

    python ${CODEBASE}/predict_on_gtex.py --vcf ${PREDVCF}  --model ${MODELDIR} --chrom ${CHROM} --outprefix predicted_gene_expression