rungweis: Routine to run a GWEIS

In GxEScanR: Run GWAS/GWEIS Scans Using Binary Dosage Files

Routine to run a GWEIS

Description

Routine to run a GWEIS

Usage

rungweis(gweismem, bdinfo, snps, outfilename, maf = 0.01)

Arguments

gweismem	Models and memory allocated by gweis-mem to run the GWEIS.
bdinfo	Information about a Binary Dosage file that contains the genetic data to run the GWEIS
snps	List of SNPs in the Binary Dosage file to perform the GWEIS on.
outfilename	Name of the file to contain the output
maf	Minimum minor allele frequency of SNPs needed to run test on.

Value

Called for its side effect of writing tab-delimited results to outfilename. Returns NULL invisibly.

Examples

## Not run: 
bdinfo <- BinaryDosage::getbdinfo(system.file("extdata", "gendata.bdose",
                                              package = "GxEScanR"))
subdata <- readRDS(system.file("extdata", "subdata.rds", package = "GxEScanR"))
subdata <- subdata[complete.cases(subdata), ]
subdata <- subdata[subdata$subid %in% bdinfo$samples$sid, ]

linearmodel <- glm(y_linear ~ x2 + x1, data = subdata)
linearmem <- gweis.mem(gemdl = linearmodel,
                       subids = subdata$subid,
                       tests = c("bg_ge", "bgxe", "joint"))
outfile <- tempfile(fileext = ".txt")
rungweis(gweismem = linearmem, bdinfo = bdinfo,
         snps = 1:nrow(bdinfo$snps), outfilename = outfile)

## End(Not run)

GxEScanR documentation built on May 1, 2026, 5:07 p.m.