ALLSPICER (version 0.1.9)

ALLSPICE: ALLSPICE

Description

ALLSPICE (ALLelic Spectrum of Pleiotropy Informed Correlated Effects)

Usage

ALLSPICE(
  data,
  pheno_corr,
  n_ind,
  gene = "GENENAME",
  pheno1 = "PHENO1",
  pheno2 = "PHENO2",
  beta1_field = "BETA1",
  beta2_field = "BETA2",
  af_field = "AF"
)

Value

A list of summary statistics from ALLSPICE test including phenotype names, gene names, MLE of slope c, ALLSPICE test statistic - lambda, pvalue from a chi-square distribution, total number of variants being tested

Arguments

data

Input data with number of rows indicating number of variants, three columns are required: 1) effect sizes of variants for phenotype 1, 2) effect sizes of variants for phenotype 2, 3) allele frequency of variants Note: this should include variants from ONE gene that is associated with the two phenotypes, preferably of the SAME functional category after being filtered to variants with allele frequency below a certain threshold (e.g. 1e-4)

pheno_corr

phenotypic correlation between the two phenotypes being tested

n_ind

total number of individuals

gene

name of the gene being tested, default `GENENAME`

pheno1

descriptive name of phenotype 1, default `PHENO1`

pheno2

descriptive name of phenotype 2, default `PHENO2`

beta1_field

field name for effect sizes of variants on phenotype 1, default `BETA1`

beta2_field

field name for effect sizes of variants on phenotype 2, default `BETA2`

af_field

field name for allele frequencies of variants, default `AF`

Examples

data <- data.frame(x = rnorm(10), y = rnorm(10), z = runif(10, 0,1))
ALLSPICE(data,pheno_corr=0.5,n_ind=10000,beta1_field='x',beta2_field='y',af_field='z')