filterMADC: Filter MADC Files

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

Filter MADC Files

Description

Filter and process MADC files to remove low quality microhaplotypes

Usage

filterMADC(
  madc_file,
  min.mean.reads = NULL,
  max.mean.reads = NULL,
  max.mhaps.per.loci = NULL,
  min.reads.per.site = 1,
  min.ind.with.reads = NULL,
  target.only = FALSE,
  n.summary.columns = NULL,
  output.file = NULL
)

Arguments

madc_file	Path to the MADC file to be filtered
min.mean.reads	Minimum mean read depth for filtering
max.mean.reads	Maximum mean read depth for filtering
max.mhaps.per.loci	Maximum number of matching mhaps per target loci. Retains only the target Ref and Alt loci at the sites that exceeds the max.mhaps.per.loci threshold.
min.reads.per.site	Minimum number of reads per site for min.ind.with.reads. Otherwise, this parameter is ignored
min.ind.with.reads	Minimum number of individuals with min.reads.per.site reads for filtering
target.only	Logical indicating whether to filter for target loci only
n.summary.columns	(optional) Number of summary columns to remove from MADC file not including the first three. Otherwise, the columns will be automatically detected and removed.
output.file	Path to save the filtered data (if NULL, data will not be saved)

Details

This function can filter raw MADC files or pre-processed MADC files with fixed allele IDs. Additionally, it can filter based on mean read depth, number of mhaps per target loci, and other criteria. Optionally, users can plot summary statistics and save the filtered data to a file.

Value

data.frame or saved csv file

Examples

#Example

#Example MADC
madc_file <- system.file("example_MADC_FixedAlleleID.csv", package="BIGr")

#Remove mhaps exceeding 3 per target region including the ref and alt target mhaps
filtered_df <- filterMADC(madc_file,
                         min.mean.reads = NULL,
                         max.mean.reads = NULL,
                         max.mhaps.per.loci = 3,
                         min.reads.per.site = 1,
                         min.ind.with.reads = NULL,
                         target.only = FALSE,
                         n.summary.columns = NULL,
                         output.file = NULL)

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