Skip to contents

Create a Physical Map from Chromosome and Position from Row Names

Source: R/extract_map.R
extract_map.Rd

This function extracts chromosome and position information from the row names of a genotype matrix. The row names are expected to follow a format where components (for example chromosome, position) are separated by a symbol (e.g., "_", "-", "."). The user can specify which part of the row name corresponds to the chromosome and position using chrom_index and pos_index, and can customize the delimiter using split_symbol.

Usage

extract_map(
  genotype_matrix,
  chrom_index = 1,
  pos_index = 2,
  markers = FALSE,
  split_symbol = "_"
)

Arguments

genotype_matrix

A matrix where:

  • Rows correspond to genetic markers.

  • Row names contain marker identifiers with multiple components separated by a delimiter (e.g., "A_1_200", "B-2-300", "C.3.400").

  • Columns correspond to individuals (not used in the function but part of the input structure).

chrom_index

Integer. The index of the chromosome identifier in the split row name. Default is 1 (first element).

pos_index

Integer. The index of the position identifier in the split row name. Default is 2 (second element).

markers

Logical. If TRUE, includes original marker names from input in the output data frame. Default is FALSE.

split_symbol

Character. The delimiter used to split the row names. Default is "_". Can be changed to "-", ".", or other valid delimiters.

Value

A data frame with columns:

  • "chrom": Chromosome identifier extracted from row names.

  • "position": Numeric genomic position extracted from row names.

  • "marker" (optional): Marker names (if markers = TRUE).

Details

  • Row names are split using the specified split_symbol to extract chromosome and position.

  • The user defines which components to extract using chrom_index and pos_index.

  • Ensures the position column is numeric.

  • If markers = TRUE, includes marker names in the output.

Examples

if (FALSE) { # \dontrun{
# Example genotype matrix with different delimiters
geno_matrix <- matrix(nrow = 3, ncol = 2)
rownames(geno_matrix) <- c("A_1_200", "B_2_300", "C_3_400")

# Default delimiter "_"
extract_map(geno_matrix)

# Using "-" as delimiter
rownames(geno_matrix) <- c("A-1-200", "B-2-300", "C-3-400")
extract_map(geno_matrix, chrom_index = 1, pos_index = 3, split_symbol = "-")
} # }