Package: mappoly 0.4.1

Marcelo Mollinari

mappoly: Genetic Linkage Maps in Autopolyploids

Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.

Authors:Marcelo Mollinari [aut, cre], Gabriel Gesteira [aut], Cristiane Taniguti [aut], Jeekin Lau [aut], Oscar Riera-Lizarazu [ctb], Guilhereme Pereira [ctb], Augusto Garcia [ctb], Zhao-Bang Zeng [ctb], Katharine Preedy [ctb, cph], Robert Gentleman [cph], Ross Ihaka [cph], R Foundation [cph], R-core [cph]

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NEWS

# Install 'mappoly' in R:

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

Bug tracker:https://github.com/mmollina/mappoly/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

hexafake - Simulated autohexaploid dataset.
hexafake.geno.dist - Simulated autohexaploid dataset with genotype probabilities.
maps.hexafake - Resulting maps from 'hexafake'
solcap.dose.map - Resulting maps from 'tetra.solcap'
solcap.err.map - Resulting maps from 'tetra.solcap'
solcap.mds.map - Resulting maps from 'tetra.solcap'
solcap.prior.map - Resulting maps from 'tetra.solcap.geno.dist'
tetra.solcap - Autotetraploid potato dataset.
tetra.solcap.geno.dist - Autotetraploid potato dataset with genotype probabilities.

On CRAN:

polyploid polyploid-genetic-mapping polyploidy

85 exports 23 stars 2.81 score 167 dependencies 1 dependents 1 mentions 330 downloads

Last updated 5 months agofrom:7bcae98fde

Exports:add_marker cache_counts_twopt calc_genoprob calc_genoprob_dist calc_genoprob_error calc_genoprob_single_parent calc_homologprob calc_prefpair_profiles check_data_sanity compare_haplotypes compare_maps cross_simulate detect_info_par dist_prob_to_class drop_marker edit_order elim_redundant est_full_hmm_with_global_error est_full_hmm_with_prior_prob est_pairwise_rf est_pairwise_rf2 est_rf_hmm est_rf_hmm_sequential export_data_to_polymapR export_map_list export_qtlpoly extract_map filter_aneuploid filter_individuals filter_map_at_hmm_thres filter_missing filter_segregation find_blocks framework_map generate_all_link_phases_elim_equivalent_haplo get_dosage_type get_genomic_order get_LOD get_submap group_mappoly import_data_from_polymapR import_from_updog import_phased_maplist_from_polymapR is.prob.data loglike_hmm ls_linkage_phases make_mat_mappoly make_pairs_mappoly make_seq_mappoly mds_mappoly merge_datasets merge_maps mf_k mp_pallet1 mp_pallet2 mp_pallet3 paralell_pairwise_discrete paralell_pairwise_probability parallel_block ph_list_to_matrix ph_matrix_to_list plot_compare_haplotypes plot_genome_vs_map plot_GIC plot_map_list plot_mappoly.map2 plot_mrk_info plot_progeny_dosage_change print_mrk read_fitpoly read_geno read_geno_csv read_geno_prob read_vcf reest_rf rev_map rf_list_to_matrix rf_snp_filter sample_data segreg_poly sim_homologous split_and_rephase summary_maps update_framework_map update_map

Dependencies:abind ape askpass backports base64enc bit bit64 bitops boot broom bslib cachem candisc car carData checkmate class cli clipr cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table dendextend Deriv digest doBy doParallel dotCall64 dplyr e1071 ellipse evaluate fansi farver fastmap fields fontawesome forcats foreach foreign Formula fs gdata generics ggplot2 ggpubr ggrepel ggsci ggsignif glmnet glue gridExtra gtable gtools haven heplots highr Hmisc hms htmlTable htmltools htmlwidgets httr isoband iterators jomo jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 magrittr maps MASS Matrix MatrixModels memoise memuse mgcv mice microbenchmark mime minqa misc3d mitml modelr munsell nlme nloptr nnet nnls numDeriv openssl ordinal pan pbkrtest permute pillar pinfsc50 pkgconfig plot3D plotly plotrix plyr polynom prettyunits princurve progress promises proxy purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen RcppParallel RCurl readr reshape2 rgl rlang rmarkdown rpart rstatix rstudioapi sass scales shape smacof spam SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex tzdb ucminf utf8 vcfR vctrs vegan viridis viridisLite vroom weights withr wordcloud xfun yaml zoo

Introduction to MAPpoly

Rendered frommappoly_startguide.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2022-11-21
Started: 2022-05-23

Help page	Topics
Add a single marker to a map	add_marker
Frequency of genotypes for two-point recombination fraction estimation	cache_counts_twopt
Compute conditional probabilities of the genotypes	calc_genoprob
Compute conditional probabilities of the genotypes using probability distribution of dosages	calc_genoprob_dist
Compute conditional probabilities of the genotypes using global error	calc_genoprob_error
Compute conditional probabilities of the genotype (one informative parent)	calc_genoprob_single_parent
Homolog probabilities	calc_homologprob
Preferential pairing profiles	calc_prefpair_profiles
Data sanity check	check_data_sanity
Compare a list of maps	compare_maps
Simulate an autopolyploid full-sib population	cross_simulate
Detects which parent is informative	detect_info_par
Remove markers from a map	drop_marker
Edit sequence ordered by reference genome positions comparing to another set order	edit_order
Eliminate redundant markers	elim_redundant
Re-estimate genetic map given a global genotyping error	est_full_hmm_with_global_error
Re-estimate genetic map using dosage prior probability distribution	est_full_hmm_with_prior_prob
Pairwise two-point analysis	est_pairwise_rf
Pairwise two-point analysis - RcppParallel version	est_pairwise_rf2
Multipoint analysis using Hidden Markov Models in autopolyploids	est_rf_hmm plot.mappoly.map print.mappoly.map
Multipoint analysis using Hidden Markov Models: Sequential phase elimination	est_rf_hmm_sequential
Export data to 'polymapR'	export_data_to_polymapR
Export a genetic map to a CSV file	export_map_list
Export to QTLpoly	export_qtlpoly
Extract the maker position from an object of class 'mappoly.map'	extract_map
Filter aneuploid chromosomes from progeny individuals	filter_aneuploid
Filter out individuals	filter_individuals
Filter missing genotypes	filter_missing
Filter markers based on chi-square test	filter_segregation
Allocate markers into linkage blocks	find_blocks
Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions.	framework_map
Genetic Mapping Functions	genetic-mapping-functions imf_h imf_k imf_m mf_h mf_k mf_m
Get the genomic position of markers in a sequence	get_genomic_order plot.mappoly.geno.ord print.mappoly.geno.ord
Extract sub-map from map	get_submap
Get table of dosage combinations	get_tab_mrks
Assign markers to linkage groups	group_mappoly
Simulated autohexaploid dataset.	hexafake
Simulated autohexaploid dataset with genotype probabilities.	hexafake.geno.dist
Import data from polymapR	import_data_from_polymapR
Import from updog	import_from_updog
Import phased map list from polymapR	import_phased_maplist_from_polymapR
Multipoint log-likelihood computation	loglike_hmm
Subset recombination fraction matrices	make_mat_mappoly
Subset pairwise recombination fractions	make_pairs_mappoly
Create a Sequence of Markers	make_seq_mappoly plot.mappoly.sequence print.mappoly.sequence
Resulting maps from 'hexafake'	maps.hexafake
Estimates loci position using Multidimensional Scaling	mds_mappoly print.mappoly.pcmap print.mappoly.pcmap3d
Merge datasets	merge_datasets
Merge two maps	merge_maps
Physical versus genetic distance	plot_genome_vs_map
Genotypic information content	plot_GIC
Plot a genetic map	plot_map_list
Plot object mappoly.map2	plot_mappoly.map2
Plot marker information	plot_mrk_info
Display genotypes imputed or changed by the HMM chain given a global genotypic error	plot_progeny_dosage_change
Plots mappoly.homoprob	plot.mappoly.homoprob
Plots mappoly.prefpair.profiles	plot.mappoly.prefpair.profiles
Summary of a set of markers	print_mrk
Data Input in fitPoly format	read_fitpoly
Data Input	plot.mappoly.data print.mappoly.data read_geno
Data Input in CSV format	read_geno_csv
Data Input	read_geno_prob
Data Input VCF	read_vcf
Re-estimate the recombination fractions in a genetic map	reest_rf
Reverse map	rev_map
Recombination fraction list to matrix	plot.mappoly.rf.matrix print.mappoly.rf.matrix rf_list_to_matrix
Remove markers that do not meet a LOD criteria	rf_snp_filter
Polysomic segregation frequency	segreg_poly
Simulate homology groups	sim_homologous
Resulting maps from 'tetra.solcap'	solcap.dose.map
Resulting maps from 'tetra.solcap'	solcap.err.map
Resulting maps from 'tetra.solcap'	solcap.mds.map
Resulting maps from 'tetra.solcap.geno.dist'	solcap.prior.map
Divides map in sub-maps and re-phase them	split_and_rephase
Summary maps	summary_maps
Autotetraploid potato dataset.	tetra.solcap
Autotetraploid potato dataset with genotype probabilities.	tetra.solcap.geno.dist
Add markers that are informative in both parents using HMM approach and evaluating difference in LOD and gap size	update_framework_map
Update map	update_map

Package: mappoly 0.4.1

mappoly: Genetic Linkage Maps in Autopolyploids

Introduction to MAPpoly

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