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geneticMapR

geneticMapR simplifies the construction of genetic maps. Built on top of MapRtools and R/qtl for reproducible analysis. Optimized for F2 diploid plant populations. Some functions were generalized for different experimental populations and polyploids. geneticMapR was designed to help with reproducible genetic map construction and quantitative trait loci (QTL) analysis.

Installation

You can install the development version of geneticMapR from GitHub with:

# Get devtools if needed
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

#Install geneticMapR
devtools::install_github("vegaalfaro/geneticMapR")

# Load library
library(geneticMapR)

Learn geneticMapR

Check out the Articles tab to learn in detail how to construct genetic maps for F2 mapping populations. Other populations under development. The vignettes (articles) are systematically designed to teach you how to create genetic maps and learn the functions along the way. geneticMapR documentation also provides some examples.

Usage

The example shows how to recode markers when neither parent is the reference genome, as is common with GBS data. Molecular markers (SNPs) must be phased to accurately trace allele inheritance in the progeny. recode is a general function that can help with that:

Recode markers 

# Load the example dataset
data("simulated_geno")

# Check markers previous to recoding
print(simulated_geno)
#>         Parent1 Parent2 F2_1 F2_2 F2_3
#> Marker1       0       2    0    1    2
#> Marker2       2       0    2    0    1
#> Marker3       0       2    1    2    1
#> Marker4       2       0    2    0    0
#> Marker5       0       2    0    2    1
#> Marker6       2       0    2    0    0

# Recode the markers using the recode() function
phased <- geneticMapR::recode(simulated_geno, parent1 = "Parent1", parent2 = "Parent2")

# Print the output
print(phased)
#>         Parent1 Parent2 F2_1 F2_2 F2_3
#> Marker1       0       2    0    1    2
#> Marker2       0       2    0    2    1
#> Marker3       0       2    1    2    1
#> Marker4       0       2    0    2    2
#> Marker5       0       2    0    2    1
#> Marker6       0       2    0    2    2

Visualization capabilities

This function generates a QTL trace plot to visualize significance scores across chromosomes for one or more traits. It highlights QTL peaks and overlays customizable vertical lines


library(geneticMapR)
data("qtl_example")

     plot_qtl_trace(qtl_df = qtl_example$qtl_df,
                thresholds_df = qtl_example$thresholds,
                  vline_df = qtl_example$vline,
                  use_physical_pos = FALSE,
                  x_angle = 0,
                trait_colors = qtl_example$colors,
                trait_labels = qtl_example$labels,
                plot_title = "Population 1")

Documentation

For detailed documentation and examples, visit geneticMapR

Credit: Adriana Lopez