Genotype-by-Environment Interaction in Polygenic Score Models

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Documentation for package ‘GxEprs’ version 1.2

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Bcov_discovery Covariate data file of the discovery dataset when the outcome is binary. This contains covariate information of the individuals in the discovery dataset following confounders.
Bcov_target Covariate data file of the target dataset when the outcome is binary. This contains covariate information of the individuals in the target dataset following confounders.
Bphe_discovery Phenotype data file of the discovery dataset when the outcome is binary. This contains phenotype information of the individuals in the discovery dataset.
Bphe_target Phenotype data file of the target dataset when the outcome is binary. This contains phenotype information of the individuals in the target dataset.
DummyData.bim PLINK .bim file
DummyData.fam PLINK .fam file
DummyData.map PLINK .map file
DummyData.ped PLINK .ped file
GWAS_binary GWAS_binary function This function performs GWAS using plink2 and outputs the GWAS summary statistics with additive SNP effects. Users may save the output in a user-specified file (see example).
GWAS_quantitative GWAS_quantitative function This function performs GWAS using plink2 and outputs the GWAS summary statistics with additive SNP effects. Users may save the output in a user-specified file (see example).
GWEIS_binary GWEIS_binary function This function performs GWEIS using plink2 and outputs the GWEIS summary statistics with additive SNP effects and interaction SNP effects. Users may save the outputs in separate user-specified files (see examples).
GWEIS_quantitative GWEIS_quantitative function This function performs GWEIS using plink2 and outputs the GWEIS summary statistics with additive SNP effects and interaction SNP effects separately. It is recommended to save the outputs in separate user-specified files (see examples).
PRS_binary PRS_binary function This function uses plink2 and outputs Polygenic Risk Scores (PRSs) of all the individuals, using pre-generated GWAS and/or GWEIS summary statistics. Note that the input used in this function can be generated by using GWAS_binary and/or GWEIS_binary functions. Users may save the output in a user-specified file (see examples).
PRS_quantitative PRS_quantitative function This function uses plink2 and outputs Polygenic Risk Scores (PRSs) of all the individuals, using pre-generated GWAS and/or GWEIS summary statistics. Note that the input used in this function can be generated by using GWAS_quantitative and/or GWEIS_quantitative functions. Users may save the output in a user-specified file (see examples).
Qcov_discovery Covariate data file of the discovery dataset when the outcome is quantitative. This contains covariate information of the individuals in the discovery dataset following confounders.
Qcov_target Covariate data file of the target dataset when the outcome is quantitative. This contains covariate information of the individuals in the target dataset following confounders.
Qphe_discovery Phenotype data file of the discovery dataset when the outcome is quantitative. This contains phenotype information of the individuals in the discovery dataset.
Qphe_target Phenotype data file of the target dataset when the outcome is quantitative. This contains phenotype information of the individuals in the target dataset.
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).
summary_permuted_quantitative summary_permuted_quantitative 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 functions. It is recommended to run this function, if you choose to fit 'PRS_gxe x E' interaction component (i.e. novel proposed model, Model 4) when generating risk scores. If the 'PRS_gxe x E' term is significant in Model 4, and insignificant in Model 4* (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).
summary_regular_binary summary_regular_binary function This function outputs the summary of regular model and final risk score values of each individual 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_binary function.
summary_regular_quantitative summary_regular_quantitative function This function outputs the summary of regular model and final risk score values of each individual 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.