get_countsMADC: Obtain Read Counts from MADC File

In BIGr: Breeding Insight Genomics Functions for Polyploid and Diploid Species

Obtain Read Counts from MADC File

Description

This function takes the MADC file as input and retrieves the ref and alt counts for each sample, and converts them to ref, alt, and size(total count) matrices for dosage calling tools. At the moment, only the read counts for the Ref and Alt target loci are obtained while the additional loci are ignored.

Usage

get_countsMADC(madc_file)

Arguments

madc_file

Path to MADC file

Value

A list of read count matrices for reference, alternate, and total read count values

Examples

# Get the path to the MADC file
madc_path <- system.file("iris_DArT_MADC.csv", package = "BIGr")

# Extract the read count matrices
counts_matrices <- get_countsMADC(madc_path)

# Access the reference, alternate, and size matrices

# ref_matrix <- counts_matrices$ref_matrix
# alt_matrix <- counts_matrices$alt_matrix
# size_matrix <- counts_matrices$size_matrix

rm(counts_matrices)

BIGr documentation built on Nov. 5, 2025, 6:03 p.m.