Package index • linkmapper

The app

run_app() run_linkmapper(): Run the Linkmapper app

Data

read_cross(): Read a genotype file
add_traits(): Add trait values to a dataset
write_mapmaker(): Write a dataset in MAPMAKER format
demo_info() linkmapper_demo(): Demo datasets
validate_lm_file(): Check that a file can be read

Quality control

qc_summary(): Marker and individual quality summary
filter_markers(): Filter markers

Linkage groups and maps

suggest_lod(): Suggest a LOD threshold
linkage_groups(): Find linkage groups
group_markers(): Group markers (Linkmapper 0.1 interface)
order_methods(): Ordering algorithms
order_groups(): Order markers within each linkage group
map_positions(): Marker positions on a map
map_summary(): Summary of each linkage group

QTL mapping

build_cross(): Build an R/qtl cross from a Linkmapper map
qtl_methods(): QTL mapping methods
scan_qtl(): Scan for QTL
genotype_effect(): Trait values by genotype at a marker

Plots

plot_effect(): Trait values by genotype
plot_linkage_map(): Draw a linkage map
plot_lod(): LOD profile plot
plot_missing(): Missing data plot
plot_rf_heatmap(): Recombination fraction heatmap for one linkage group
plot_segregation(): Segregation test plot
map_plot_size(): Size of a linkage map figure in inches
theme_linkmapper(): ggplot2 theme used by Linkmapper

Analyses, reports and sessions

default_settings(): Default analysis settings
run_analysis(): Run a whole analysis from settings
build_script(): Write an R script that repeats an analysis
build_report(): Write a self-contained HTML report
save_session() load_session(): Save and restore an analysis session

Package

linkmapper linkmapper-package: linkmapper: Point-and-Click Linkage Mapping and QTL Analysis