level_function {GWAS.BAYES} | R Documentation |
Removes all SNPs that only have one level in it
level_function(SNPs,MAF = 0.01)
SNPs |
The standardized SNP data where the columns take on the values of 0 or 1 |
MAF |
The minor allele frequency at which to drop SNPs. Default is set to 0.01, meaning if the minor allele occurs less than 1 percent of the time in a given SNP, that given SNP will be dropped from the dataset. |
SNPs |
The SNP matrix where columns that were either all 1's or all 0's are removed |
SNPs_Dropped |
A true/false vector with length ncol(SNPs), where the TRUE's indicate that the column was not dropped and the FALSE's indicate that the column was dropped |
data("vignette_lm_dat") Y <- vignette_lm_dat$Phenotype SNPs <- vignette_lm_dat[,-1] SNPs <- standardize(SNPs = SNPs,method = "major-minor",number_cores = 1) list1 <- aggregate_SNPs(SNPs = SNPs, Y = Y) SNPs <- list1[[1]] Y <- list1[[2]] level_function(SNPs, MAF = .01)