GxEprs (version 1.1)

summary_permuted_binary: summary_permuted_binary function This function outputs the p value of permuted model in the target dataset, using pre-generated Polygenic Risk Scores (PRSs) of all the individuals. Note that the input used in this function can be generated by using PRS_quantitative function. It is recommended to run this function, if you choose to fit 'PRS_gxe x E' interaction component (i.e. novel proposed model, Model 5) when generating risk scores. If the 'PRS_gxe x E' term is significant in Model 5, and insignificant in Model 5* (permuted p value), consider that the 'PRS_gxe x E' interaction component is actually insignificant (always give priority to the p value obtained from the permuted model).

Description

summary_permuted_binary function This function outputs the p value of permuted model in the target dataset, using pre-generated Polygenic Risk Scores (PRSs) of all the individuals. Note that the input used in this function can be generated by using PRS_quantitative function. It is recommended to run this function, if you choose to fit 'PRS_gxe x E' interaction component (i.e. novel proposed model, Model 5) when generating risk scores. If the 'PRS_gxe x E' term is significant in Model 5, and insignificant in Model 5* (permuted p value), consider that the 'PRS_gxe x E' interaction component is actually insignificant (always give priority to the p value obtained from the permuted model).

Usage

summary_permuted_binary(
  Bphe_target,
  Bcov_target,
  iterations = 1000,
  add_score,
  gxe_score
)

Value

This function will output

B_permuted_p

the p value of the permuted model

Arguments

Bphe_target

Phenotype file containing family ID, individual ID and phenotype of the target dataset as columns, without heading

Bcov_target

Covariate file containing family ID, individual ID, standardized covariate, square of standardized covariate, and/or confounders of the target dataset as columns, without heading

iterations

Number of iterations used in permutation

add_score

PRSs generated using additive SNP effects of GWEIS summary statistics

gxe_score

PRSs generated using interaction SNP effects of GWEIS summary statistics

Examples

if (FALSE) { 
a <- GWEIS_binary(plink_path, DummyData, Bphe_discovery, Bcov_discovery)
add <- a[c("ID", "A1", "ADD_OR")]
gxe <- a[c("ID", "A1", "INTERACTION_OR")]
p <- PRS_binary(plink_path, DummyData, summary_input = add)
q <- PRS_binary(plink_path, DummyData, summary_input = gxe)
x <- summary_permuted_binary(Bphe_target, Bcov_target, iterations = 1000, 
add_score = p, gxe_score = q)
x
}