convertgen | R Documentation |
Convert genotypes in HapMap format or in numeric format for hypred package.
convertgen( input_geno, type = c("hmp1", "hmp2", "num"), missingrate = 0.2, maf = 0.05, impute = TRUE )
input_geno |
genotype in HapMap format or in numeric format. The names of individuals should be provided. Missing (NA) values are allowed. |
type |
the type of genotype. There are three options: "hmp1" for genotypes in HapMap format with single bit, "hmp2" for genotypes in HapMap format with double bit, and "num" for genotypes in numeric format. |
missingrate |
max missing percentage for each SNP, default is 0.2. |
maf |
minor allele frequency for each SNP, default is 0.05. |
impute |
logical. If TRUE, imputation. Default is TRUE. |
A matrix of genotypes in numeric format, coded as 1, 0, -1 for AA, Aa, aa. Each row represents an individual and each column represents a marker. The rownames of the matrix are the names of individuals.
## load genotype in HapMap format with double bit data(input_geno) ## convert genotype for hypred package inbred_gen <- convertgen(input_geno, type = "hmp2") ## load genotype in numeric format data(input_geno1) head(input_geno1) ## convert genotype for hypred package inbred_gen1 <- convertgen(input_geno1, type = "num")
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