Package index • geneticMapR

Core Functions

convert_to_dosage_advanced(): Convert VCF Genotype Format to Dosage (Advanced, Polyploid-Compatible)

effect_plot(): Powerful Effect Plots

estimate_map(): Estimate Genetic Map Positions

extract_map(): Create a Physical Map from Chromosome and Position from Row Names

freq(): Calculate Genotype Frequency Per Individual or Marker

get_LOD_int(): Get LOD Support Intervals for QTL Peaks (Single or Multiple Traits)

haplotype_reconstruction(): F2 diploid population Haplotype Reconstruction

recode(): Phase Genotype Marker Data Based on Parental References

simple_effect_plot(): Simple Effect Plot

trim_LG(): Trim Linkage Groups Based on LOD Thresholds

Filtering, Formatting and Plotting

filter_geno_by_freq(): Filter Genotype Matrix by Allele Frequency

filter_geno_by_freq_poly(): Filter Genotype Matrix by Dosage Frequency (Polyploid-Compatible)

filter_geno_by_parents(): Filter Genotype Matrix Based on Parental Genotype

filter_missing_geno(): Filter Markers or Individuals Based on Missing Genotype Data

formater(): Convert Between Character (A, H, B) and Numeric dosage (0, 1, 2) Formats

formater_flex(): Flexible Genotype Format Converter (Supports Polyploid Dosage)

format_qtl_input(): Format Input Data for R/qtl package

LD_decay_plot(): Plot LD vs distance

frequency_plot(): Generate a Histogram of Genotype Frequencies

order_and_plot(): Optimize Marker Order

plotMap_gg(): Plot Genetic Map Using ggplot2 in R/qtl data environment

plot_qtl_trace(): Generates a line plot showing QTL traces (LOD scores) across chromosomes for one or more traits. Supports customization of visual appearance and annotations such as significance thresholds and vertical lines.

plot_coverage(): Plot Genome-wide Coverage

plot_genotype_histogram(): Plot a Histogram of Genotypic Values

plot_marey(): Generate a Marey Plot for one Chromosome

plot_reconstructed_haplo(): Plot Haplotype Reconstruction Results Before and After HMM

Data

simulated_geno: Simulated Simple Genotype Matrix Dataset

qtl_example: QTL Dataset Example

Utility Functions

convert_to_dosage(): Convert VCF Genotype Format to Dosage for Diploids

convert_to_dosage_flex(): Convert VCF Genotype Format to Dosage (Supports Polyploids and Missing Alleles)

drop_parents(): Drop Parents and F1 Individuals from a Data Frame

melt_freq(): Convert (Melt) Genotype Frequency Data to Long Format

rename_geno_matrix(): Rename Parents, F1, and F2 Individuals in a Genotype Matrix

estimate_error(): Estimate Genotyping Error Rate