Package: linkmapper 0.2.0

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

A 'shiny' application and a set of plain R functions for building genetic linkage maps and locating quantitative trait loci in F2 intercross, backcross and recombinant inbred line populations. It wraps 'onemap' (Margarido et al. 2007 <doi:10.1111/j.2007.0018-0661.02000.x>) for segregation tests, two-point analysis, grouping, ordering and map estimation, and 'qtl' (Broman et al. 2003 <doi:10.1093/bioinformatics/btg112>) for interval mapping and composite interval mapping with permutation thresholds. Results can be exported as figures, tables, a self-contained HTML report and an R script that reproduces the analysis.

Authors:Ebenezer Ogoe [aut, cre, cph], Michael Obeng [aut, cph], Stephen Amoako [aut, cph]

linkmapper_0.2.0.tar.gz
linkmapper_0.2.0.zip(r-4.7-any)linkmapper_0.2.0.zip(r-4.6-any)linkmapper_0.2.0.zip(r-4.5-any)
linkmapper_0.2.0.tgz(r-4.6-any)linkmapper_0.2.0.tgz(r-4.5-any)
linkmapper_0.2.0.tar.gz(r-4.7-any)linkmapper_0.2.0.tar.gz(r-4.6-any)
linkmapper_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
linkmapper/json (API)

# Install 'linkmapper' in R:

install.packages('linkmapper', repos = c('https://ebenogoe.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ebenogoe/linkmapper/issues

Pkgdown/docs site:https://ebenogoe.github.io

On CRAN:

gene-map linkage-mapping open-source qtl-mapping r-shiny

2.00 score 35 exports 187 dependencies

Last updated from:a75c2a9a05 (on main). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	187
source / vignettes	OK	244
linux-release	OK	188
macos-release	OK	122
macos-oldrel	OK	131
windows-devel	OK	117
windows-release	OK	117
windows-oldrel	OK	125
wasm-release	OK	153

Exports:add_traits build_cross build_report build_script default_settings demo_info filter_markers genotype_effect group_markers linkage_groups linkmapper_demo load_session map_plot_size map_positions map_summary order_groups order_methods plot_effect plot_linkage_map plot_lod plot_missing plot_rf_heatmap plot_segregation qc_summary qtl_methods read_cross run_analysis run_app run_linkmapper save_session scan_qtl suggest_lod theme_linkmapper validate_lm_file write_mapmaker

Dependencies:abind ape askpass assertthat attempt backports base64enc bit bit64 boot broom bsicons bslib cachem car carData checkmate cicerone class cli clipr cluster codetools colorspace commonmark config corrplot cowplot cpp11 crayon crosstalk curl data.table dendextend Deriv digest doBy doParallel dplyr e1071 ellipse evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach forecast foreign Formula fracdiff fs gdata gdtools generics ggiraph ggplot2 ggpubr ggrepel ggsci ggsignif glmnet glue golem gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr isoband iterators jomo jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels memoise memuse mgcv mice mime minqa mitml modelr nlme nloptr nnet nnls numDeriv onemap openssl ordinal otel pan pbkrtest permute pillar pinfsc50 pkgconfig plotly plotrix plyr polynom prettyunits princurve progress promises proxy purrr qtl quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reactable reactR readr reformulas reshape2 rlang rmarkdown rpart rstatix rstudioapi S7 sass scales shape shiny smacof sourcetools SparseM stringi stringr survival svglite sys systemfonts textshaping tibble tidyr tidyselect timeDate tinytex tzdb ucminf urca utf8 vcfR vctrs vegan viridis viridisLite vroom weights withr wordcloud writexl xfun xtable yaml zoo

Help page	Topics
Add trait values to a dataset	add_traits
Build an R/qtl cross from a Linkmapper map	build_cross
Write a self-contained HTML report	build_report
Write an R script that repeats an analysis	build_script
Default analysis settings	default_settings
Demo datasets	demo_info linkmapper_demo
Filter markers	filter_markers
Trait values by genotype at a marker	genotype_effect
Group markers (Linkmapper 0.1 interface)	group_markers
Find linkage groups	linkage_groups
Size of a linkage map figure in inches	map_plot_size
Marker positions on a map	map_positions
Summary of each linkage group	map_summary
Order markers within each linkage group	order_groups
Ordering algorithms	order_methods
Trait values by genotype	plot_effect
Draw a linkage map	plot_linkage_map
LOD profile plot	plot_lod
Missing data plot	plot_missing
Recombination fraction heatmap for one linkage group	plot_rf_heatmap
Segregation test plot	plot_segregation
Marker and individual quality summary	qc_summary
QTL mapping methods	qtl_methods
Read a genotype file	read_cross
Run a whole analysis from settings	run_analysis
Run the Linkmapper app	run_app run_linkmapper
Save and restore an analysis session	load_session save_session
Scan for QTL	scan_qtl
Suggest a LOD threshold	suggest_lod
ggplot2 theme used by Linkmapper	theme_linkmapper
Check that a file can be read	validate_lm_file
Write a dataset in MAPMAKER format	write_mapmaker

Package: linkmapper 0.2.0

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

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