User guide

GPSEA allows users to perform many different kinds of genotype-phenotype correlation (GPCs) analysis. See the Tutorial for an introduction. In general, the analysis will include steps for data input, exploration of the cohort to assist in generating hypotheses about potential GPCs to test, corresponding choice of genotype and phenotype predicates to perform the test, choice of statistical test, and approach to multiple-testing correction (mtc). The pages shown in the table of contents provide more information about each step.

Contents:

• Input data
  • Standardize genotype and phenotype data
    • Create a cohort from GA4GH phenopackets
  • Persist the cohort for later
    • Example
  • Choose the transcript and protein of interest
    • Choose the transcript
    • Get the transcript data
    • Fetch protein data
  • Plot distribution of cohort variants on the protein
    • Example
• Cohort exploratory analysis
  • Types of statistical test
  • Power
  • Exploration
    • Interactive exploration
    • Cohort summary
    • Distribution of variants across protein domains
    • Plot distribution of variants with respect to the protein sequence
• Predicates
  • Genotype Predicates
    • Variant Predicates
    • Group by variant category
    • Group by allele count
    • Group by sex
    • Group by diagnosis
  • Phenotype Predicates
    • HPO predicate
    • Predicates for all cohort phenotypes
    • De Vries Score
  • Gallery
  • Need more?
• Statistical analyses
  • Compare genotype and phenotype groups
    • Fisher exact test (FET)
    • Example analysis
  • Compare phenotype scores in genotype groups
    • Mann-Whitney U Test
    • Example analysis
  • Compare measurement values
    • Example analysis
  • Survival analysis
    • Example analysis
• Multiple-testing correction
  • Background
  • Implementation in GPSEA
    • Multiple-testing correction procedures
    • MT filters: Choosing which terms to test
• General HPO terms
• Glossary
  • True path rule
  • Length of the reference allele
  • Change length of an allele