Convert a 0/1/2 genotype matrix into a VCF-like format

This function converts a genotype matrix encoded as 0,1,2 into a VCF-like format. It can either return the VCF content as a data.frame, write it to a .vcf file or do both.

Usage

transform_geno_into_vcf(
  geno_matrix,
  output_type = c("file", "dataframe", "both"),
  output_path = NULL
)

Arguments

geno_matrix

A matrix of genotypes with values 0, 1, 2. SNPs are in rows and individuals in columns.

output_type

A character, that specifies the output type. Choose between "file" (write .vcf), "dataframe" (return data.frame), or "both" (do both).

output_path

A character string that specifies the output path. Requiered if output_type is "file" or "both".

Value

A data.frame if output_type = "dataframe" or "both", or just write the .vcf file if output_type = "file" or "both".

Examples

n_ind <- 50
n_snp <- 50

# Create a little genotype matrix
set.seed(123)
geno_matrix <- matrix(sample(0:2, size = n_ind*n_snp, replace = TRUE),
                      nrow = n_snp, ncol = n_ind)

# Transform genotype matrix into VCF
vcf <- transform_geno_into_vcf(geno_matrix, output_type = "dataframe")
head(vcf[1:3,1:7])
#>   CHROM POS  ID REF ALT QUAL FILTER
#> 1     1   1 rs1   A   T    .      .
#> 2     1   2 rs2   A   T    .      .
#> 3     1   3 rs3   A   T    .      .