GxEprs (version 1.1)

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).

Description

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).

Usage

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

Value

This function will perform GWAS and output

Q_out.trd.sum

GWAS summary statistics with additive 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

Name (with file extension) of the phenotype file containing family ID, individual ID and phenotype of the discovery dataset as columns, without heading

Qcov_discovery

Name (with file extension) of the 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 <- GWAS_quantitative(plink_path, DummyData, Qphe_discovery, Qcov_discovery, 
thread = 20)
sink("Q_out.trd.sum") #to create a file in the working directory
write.table(x[c("ID", "A1", "BETA")], sep = " ", 
row.names = FALSE, quote = FALSE) #to write the output
sink() #to save the output
head(x) #to obtain the head of GWAS summary statistics of additive 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$OBS_CT #to extract the number of allele observations 
x$BETA #to extract the SNP effects
x$SE #to extract the standard errors of the SNP effects
x$T_STAT #to extract the test statistics 
x$P #to extract the p values 
}