merge_MADCs: Merge MADC files

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

Merge MADC files

Description

If duplicated samples exist in different files, a suffix will be added at the end of the sample name. If run_ids is defined, they are used as suffix, if not, files will be identified from 1 to number of files, considering the order that was defined in the function.

Usage

merge_MADCs(..., madc_list = NULL, out_madc = NULL, run_ids = NULL)

Arguments

...	one or more MADC files path
madc_list	list containing path to MADC files to be merged
out_madc	output merged MADC file path
run_ids	vector of character defining the run ID for each file. This ID will be added as a suffix in repeated sample ID in case they exist in different files.

Value

A data frame containing the merged MADC data. The merged file is also written to the specified out_madc path in CSV format. Numeric columns are filled with zeros where data is missing.

Examples

# First generating example MADC files
temp_dir <- tempdir()
file1_path <- file.path(temp_dir, "madc1.csv")
file2_path <- file.path(temp_dir, "madc2.csv")
out_path <- file.path(temp_dir, "merged_madc.csv")

# Data for file 1: Has SampleA and SampleB
df1 <- data.frame(
  AlleleID = c("chr1.1_0001|Alt_0002", "chr1.1_0001|Ref_0001", "chr1.1_0001|AltMatch_0001"),
  CloneID = c("chr1.1_0001", "chr1.1_0001", "chr1.1_0001"),
  AlleleSequence = c("GGG", "AAA", "TTT"),
  SampleA = c(10, 8, 0),
  SampleB = c(5, 4, 9),
  stringsAsFactors = FALSE,
  check.names = FALSE
)
write.csv(df1, file1_path, row.names = FALSE, quote = FALSE)

# Data for file 2: Has SampleA (duplicate name) and SampleC, different rows
df2 <- data.frame(
  AlleleID = c("chr1.1_0001|Alt_0002", "chr1.1_0001|Ref_0001", "chr1.1_0001|AltMatch_0001"),
  CloneID = c("chr1.1_0001", "chr1.1_0001", "chr1.1_0001"),
  AlleleSequence = c("GGG", "AAA", "TTT"),
  SampleA = c(11, 7, 20),
  SampleC = c(1, 2, 6),
  stringsAsFactors = FALSE,
  check.names = FALSE
)
write.csv(df2, file2_path, row.names = FALSE, quote = FALSE)

# 2. Run the merge function
# Use default suffixes (.x, .y) for the duplicated "SampleA"
merge_MADCs(madc_list = list(file1_path, file2_path),
            out_madc = out_path)

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