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Perform association tests between phenotype risk scores and genotypes

Source: R/genetic_association.R
getGeneticAssociations.Rd

The association test for each disease-variant pair is based on a linear model, with the phenotype risk score as the dependent variable.

Usage

getGeneticAssociations(
  scores,
  genotypes,
  demos,
  diseaseVariantMap,
  lmFormula,
  modelType = c("genotypic", "additive", "dominant", "recessive"),
  level = 0.95,
  dopar = FALSE
)

Arguments

scores

A data.table of phenotype risk scores. Must have columns person_id, disease_id, score.

genotypes

A matrix or 'BEDMatrix' object containing genetic data, with rownames corresponding to person_ids in demos and scores, and colnames corresponding to variant_ids in diseaseVariantMap.

demos

A data.table of characteristics for each person in the cohort. Must have column person_id.

diseaseVariantMap

A data.table indicating which genetic variants to test for association with phenotype risk scores for which diseases. Must have columns disease_id and variant_id.

lmFormula

A formula representing the linear model (excluding the term for genotype) to use for the association tests. All terms in the formula must correspond to columns in demos.

modelType

A string indicating how to encode genotype in the model.

level

A number indicating the level of the confidence interval. Default is 0.95.

dopar

Logical indicating whether to run calculations in parallel if a parallel backend is already set up, e.g., using doParallel::registerDoParallel(). Recommended to minimize runtime.

Value

A data.table of statistics for the association tests (if a model fails to converge, NAs will be reported):

  • disease_id: Disease identifier

  • variant_id: Variant identifier

  • n_total: Number of persons with non-missing genotype data for the given variant.

  • n_wt: Number of persons homozygous for the wild-type allele.

  • n_het: Number of persons having one copy of the alternate allele.

  • n_hom: Number of persons homozygous for the alternate allele.

  • beta: Coefficient for the association of genotype with score

  • se: Standard error for beta

  • pval: P-value for beta being non-zero

  • ci_lower: Lower bound of the confidence interval for beta

  • ci_upper: Upper bound of the confidence interval for beta

If modelType is "genotypic", the data.table will include separate statistics for heterozygous and homozygous genotypes.

See also

stats::lm(), stats::confint(), getScores()

Examples

library('data.table')
library('BEDMatrix')

# map ICD codes to phecodes
phecodeOccurrences = getPhecodeOccurrences(icdSample)

# calculate weights
weights = getWeights(demoSample, phecodeOccurrences)

# OMIM disease IDs for which to calculate phenotype risk scores
diseaseId = 154700

# map diseases to phecodes
diseasePhecodeMap = mapDiseaseToPhecode()

# calculate scores
scores = getScores(weights, diseasePhecodeMap[disease_id == diseaseId])

# map diseases to genetic variants
nvar = 10
diseaseVariantMap = data.table(disease_id = diseaseId, variant_id = paste0('snp', 1:nvar))

# load sample genetic data
npop = 50
genoSample = BEDMatrix(system.file('extdata', 'geno_sample.bed', package = 'phers'))
#> Extracting number of samples and rownames from geno_sample.fam...
#> Extracting number of variants and colnames from geno_sample.bim...
colnames(genoSample) = paste0('snp', 1:nvar)
rownames(genoSample) = 1:npop

# run genetic association tests
genoStats = getGeneticAssociations(
  scores, genoSample, demoSample, diseaseVariantMap, lmFormula = ~ sex,
  modelType = 'additive')