Welcome to GPRS documentation!

Tutorials

• About gprs package
  • Environment setup
• Get started: understanding the data format
  • GWAS template
  • GeneAtlas template
  • How to choose model template?
• Before step1:
• Step1: Unify the data format
  • Function: gprs geneatlas-filter-data
  • How to use it?
  • output files
• Setp 2: Generate Plink bfiles (.bim, .bam, .fam)
  • Function: gprs generate-plink-bfiles
  • How to use it?
  • output files
• Setp 3-1: Clumping (remove linked SNPs)
  • Function: gprs clump
  • How to use it?
  • output files
• Setp 3-2: Filter SNPs depends on .clump
  • Function: gprs select-clump-snps
  • How to use it?
  • output files
  • With Chromosome information:
  • Without Chromosome information:
• Setp 4-1: Generate PRS model
  • Function: gprs build-prs
  • How to use it?
  • output files
• Setp 4-2: Combined PRS model
  • Function:gprs combine-prs
  • How to use it?
  • output files
• Setp 5-1: Calculate statistics value of PRS model
  • Function: prs-statistics
  • How to use it?
  • output files
• Setp 5-2: Combined PRS statistics results (Optional)
  • Function:combine-prs-stat
  • How to use it?
  • output files

Examples

• Example of giant height from Wood et al 2014
  • Get started: 2014 height data structure
  • The data structure:
  • Which template to use?
  • Output folders
  • Step1 preparing data set - unified the data format
  • After preparing the data-set three files obtained
  • Step2 use qc’d SNPs list to obtain Plink bfiles(.bed, .bim, .fam)
  • Step3.1 remove linked SNPs
  • Step3.2 select clumped SNPs
  • Step4.1 Generate PRS model
  • Step4.2 Combined PRS model
  • Visualize distribution of PRS in each population
• Example of MEC American Africans

API Reference

• GPRS
• GeneAtlasModel
• GwasModel

Indices and tables

• Index

• Module Index

• Search Page