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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

polyploidpolyploid-genetic-mappingpolyploidy

85 exports 23 stars 2.71 score 176 dependencies 1 dependents 356 downloads

Last updated 3 months agofrom:7bcae98fdeaeb4538a8f087cb7f92386399b9bdb

Exports:add_markercache_counts_twoptcalc_genoprobcalc_genoprob_distcalc_genoprob_errorcalc_genoprob_single_parentcalc_homologprobcalc_prefpair_profilescheck_data_sanitycompare_haplotypescompare_mapscross_simulatedetect_info_pardist_prob_to_classdrop_markeredit_orderelim_redundantest_full_hmm_with_global_errorest_full_hmm_with_prior_probest_pairwise_rfest_pairwise_rf2est_rf_hmmest_rf_hmm_sequentialexport_data_to_polymapRexport_map_listexport_qtlpolyextract_mapfilter_aneuploidfilter_individualsfilter_map_at_hmm_thresfilter_missingfilter_segregationfind_blocksframework_mapgenerate_all_link_phases_elim_equivalent_haploget_dosage_typeget_genomic_orderget_LODget_submapgroup_mappolyimport_data_from_polymapRimport_from_updogimport_phased_maplist_from_polymapRis.prob.dataloglike_hmmls_linkage_phasesmake_mat_mappolymake_pairs_mappolymake_seq_mappolymds_mappolymerge_datasetsmerge_mapsmf_kmp_pallet1mp_pallet2mp_pallet3paralell_pairwise_discreteparalell_pairwise_probabilityparallel_blockph_list_to_matrixph_matrix_to_listplot_compare_haplotypesplot_genome_vs_mapplot_GICplot_map_listplot_mappoly.map2plot_mrk_infoplot_progeny_dosage_changeprint_mrkread_fitpolyread_genoread_geno_csvread_geno_probread_vcfreest_rfrev_maprf_list_to_matrixrf_snp_filtersample_datasegreg_polysim_homologoussplit_and_rephasesummary_mapsupdate_framework_mapupdate_map

Dependencies:abindapeaskpassbackportsbase64encbitbit64bitopsbootbriobroombslibcachemcallrcandisccarcarDatacheckmateclassclicliprclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextenddescdiffobjdigestdoParalleldotCall64dplyre1071ellipseevaluatefansifarverfastmapfieldsfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2ggpubrggrepelggsciggsignifglmnetgluegridExtragtablegtoolshavenheplotshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjomojquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrmapsMASSMatrixMatrixModelsmemoisememusemgcvmicemimeminqamisc3dmitmlmunsellnlmenloptrnnetnnlsnumDerivopensslordinalpanpbkrtestpermutepillarpinfsc50pkgbuildpkgconfigpkgloadplot3DplotlyplotrixplyrpolynompraiseprettyunitsprincurveprocessxprogresspromisesproxypspurrrquantregR6rappdirsRColorBrewerRcppRcppEigenRcppParallelRCurlreadrrematch2reshape2rglrlangrmarkdownrpartrprojrootrstatixrstudioapisassscalesshapesmacofspamSparseMstringistringrsurvivalsystestthattibbletidyrtidyselecttinytextzdbucminfutf8vcfRvctrsveganviridisviridisLitevroomwaldoweightswithrwordcloudxfunyamlzoo

mappoly_intro

Rendered frommappoly_startguide.Rmdusingknitr::rmarkdownon Jun 04 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Add a single marker to a mapadd_marker
Frequency of genotypes for two-point recombination fraction estimationcache_counts_twopt
Compute conditional probabilities of the genotypescalc_genoprob
Compute conditional probabilities of the genotypes using probability distribution of dosagescalc_genoprob_dist
Compute conditional probabilities of the genotypes using global errorcalc_genoprob_error
Compute conditional probabilities of the genotype (one informative parent)calc_genoprob_single_parent
Homolog probabilitiescalc_homologprob
Preferential pairing profilescalc_prefpair_profiles
Data sanity checkcheck_data_sanity
Compare a list of mapscompare_maps
Simulate an autopolyploid full-sib populationcross_simulate
Detects which parent is informativedetect_info_par
Remove markers from a mapdrop_marker
Edit sequence ordered by reference genome positions comparing to another set orderedit_order
Eliminate redundant markerselim_redundant
Re-estimate genetic map given a global genotyping errorest_full_hmm_with_global_error
Re-estimate genetic map using dosage prior probability distributionest_full_hmm_with_prior_prob
Pairwise two-point analysisest_pairwise_rf
Pairwise two-point analysis - RcppParallel versionest_pairwise_rf2
Multipoint analysis using Hidden Markov Models in autopolyploidsest_rf_hmm plot.mappoly.map print.mappoly.map
Multipoint analysis using Hidden Markov Models: Sequential phase eliminationest_rf_hmm_sequential
Export data to 'polymapR'export_data_to_polymapR
Export a genetic map to a CSV fileexport_map_list
Export to QTLpolyexport_qtlpoly
Extract the maker position from an object of class 'mappoly.map'extract_map
Filter aneuploid chromosomes from progeny individualsfilter_aneuploid
Filter out individualsfilter_individuals
Filter missing genotypesfilter_missing
Filter markers based on chi-square testfilter_segregation
Allocate markers into linkage blocksfind_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 Functionsgenetic-mapping-functions imf_h imf_k imf_m mf_h mf_k mf_m
Get the genomic position of markers in a sequenceget_genomic_order plot.mappoly.geno.ord print.mappoly.geno.ord
Extract sub-map from mapget_submap
Get table of dosage combinationsget_tab_mrks
Assign markers to linkage groupsgroup_mappoly
Simulated autohexaploid dataset.hexafake
Simulated autohexaploid dataset with genotype probabilities.hexafake.geno.dist
Import data from polymapRimport_data_from_polymapR
Import from updogimport_from_updog
Import phased map list from polymapRimport_phased_maplist_from_polymapR
Multipoint log-likelihood computationloglike_hmm
Subset recombination fraction matricesmake_mat_mappoly
Subset pairwise recombination fractionsmake_pairs_mappoly
Create a Sequence of Markersmake_seq_mappoly plot.mappoly.sequence print.mappoly.sequence
Resulting maps from 'hexafake'maps.hexafake
Estimates loci position using Multidimensional Scalingmds_mappoly print.mappoly.pcmap print.mappoly.pcmap3d
Merge datasetsmerge_datasets
Merge two mapsmerge_maps
Physical versus genetic distanceplot_genome_vs_map
Genotypic information contentplot_GIC
Plot a genetic mapplot_map_list
Plot object mappoly.map2plot_mappoly.map2
Plot marker informationplot_mrk_info
Display genotypes imputed or changed by the HMM chain given a global genotypic errorplot_progeny_dosage_change
Plots mappoly.homoprobplot.mappoly.homoprob
Plots mappoly.prefpair.profilesplot.mappoly.prefpair.profiles
Summary of a set of markersprint_mrk
Data Input in fitPoly formatread_fitpoly
Data Inputplot.mappoly.data print.mappoly.data read_geno
Data Input in CSV formatread_geno_csv
Data Inputread_geno_prob
Data Input VCFread_vcf
Re-estimate the recombination fractions in a genetic mapreest_rf
Reverse maprev_map
Recombination fraction list to matrixplot.mappoly.rf.matrix print.mappoly.rf.matrix rf_list_to_matrix
Remove markers that do not meet a LOD criteriarf_snp_filter
Polysomic segregation frequencysegreg_poly
Simulate homology groupssim_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 themsplit_and_rephase
Summary mapssummary_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 sizeupdate_framework_map
Update mapupdate_map