GxEprs (version 1.1)

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).

Description

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).

Usage

GWEIS_quantitative(
  plink_path,
  b_file,
  Qphe_discovery,
  Qcov_discovery,
  thread = 20
)

Value

This function will perform GWEIS and output

Q_out.sum

GWEIS summary statistics with additive and interaction SNP effects

Arguments

plink_path

Path to the PLINK executable application

b_file

Prefix of the binary files, where all .fam, .bed and .bim files have a common prefix

Qphe_discovery

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

Qcov_discovery

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

thread

Number of threads used

Examples

if (FALSE) { 
x <- GWEIS_quantitative (plink_path, DummyData, Qphe_discovery, Qcov_discovery, 
thread = 20)
sink("Q_out.add.sum") #to create a file in the working directory
write.table(x[c("ID", "A1", "ADD_BETA")], sep = " ", 
row.names = FALSE, quote = FALSE) #to write the output
sink() #to save the output
sink("Q_out.gxe.sum") #to create a file in the working directory
write.table(x[c("ID", "A1", "INTERACTION_BETA")], sep = " ", 
row.names = FALSE, quote = FALSE) #to write the output
sink() #to save the output
head(x) #to extract the head of all columns in GWEIS summary  
#statistics of additive and interaction SNP effects 
x$CHROM #to extract the chromosome number 
x$POS #to extract the base pair position
x$ID #to extract the SNP ID
x$REF #to extract the reference allele
x$ALT #to extract the alternate allele 
x$A1 #to extract the minor allele
x$OBS_CT #to extract the number of allele observations 
x$ADD_BETA #to extract the additive SNP effects
x$ADD_SE #to extract the standard errors of the 
#additive SNP effects
x$ADD_T_STAT #to extract the test statistics of additive 
#SNP effects
x$ADD_P #to extract the p values of additive SNP effects
x$INTERACTION_BETA #to extract the interaction SNP effects
x$INTERACTION_SE #to extract the standard errors of the 
#interaction SNP effects
x$INTERACTION_T_STAT #to extract the test statistics of 
#interaction SNP effects
x$INTERACTION_P #to extract the p values of interaction 
#SNP effects
}