ALLSPICE {ALLSPICER}R Documentation

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"
)

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'

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

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')

[Package ALLSPICER version 0.1.9 Index]