GWEIS_binary {GxEprs} | R Documentation |
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).
Description
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).
Usage
GWEIS_binary(plink_path, b_file, Bphe_discovery, Bcov_discovery, thread = 20)
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 |
Bphe_discovery |
Phenotype file containing family ID, individual ID and phenotype of the discovery dataset as columns, without heading |
Bcov_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 |
Value
This function will perform GWEIS and output
B_out.sum |
GWEIS summary statistics with additive and interaction SNP effects |
Examples
## Not run:
x <- GWEIS_binary(plink_path, DummyData, Bphe_discovery, Bcov_discovery,
thread = 20)
sink("B_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("B_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_Z_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_Z_STAT #to extract the test statistics of
#interaction SNP effects
x$INTERACTION_P #to extract the p values of interaction
#SNP effects
## End(Not run)