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')