Package: polymapR 1.1.6

polymapR: Linkage Analysis in Outcrossing Polyploids

Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Authors:Peter Bourke [aut, cre], Geert van Geest [aut], Roeland Voorrips [ctb], Yanlin Liao [ctb]

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# Install 'polymapR' in R:
install.packages('polymapR', repos = c('https://pbourkey.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.51 score 1 stars 54 scripts 751 downloads 50 exports 122 dependencies

Last updated 6 months agofrom:2310636196. Checks:OK: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winERROROct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:add_dup_markersassign_linkage_groupassign_SN_SNbridgeHomologuescalcSegtypeInfocheck_mapcheck_marker_assignmentcheck_maxPcheckF1cluster_per_LGcluster_SN_markerscompare_mapsconsensus_LG_assignmentconsensus_LG_namesconvert_marker_dosagesconvert_polyRADconvert_updogcorrectDosagescreate_phased_maplistcreateTetraOriginInputdefine_LG_structurefinish_linkage_analysisget_markertype_combinationsgp_overviewhomologue_lg_assignmentlinkagelinkage.gpmarker_binningmarker_data_summaryMDSMap_from_listmerge_homologuesoverviewSNlinksparental_quantitiesPCA_progenyphase_SN_diploidplot_hom_vs_LGplot_mapplot_phased_maplistr_LOD_plotscreen_for_duplicate_individualsscreen_for_duplicate_individuals.gpscreen_for_duplicate_markersscreen_for_NA_valuesSNSN_LOD_deviationstest_prefpairingwrite_nested_listwrite_pwd_listwrite.mctwrite.pwdwrite.TSNPM

Dependencies:backportsbase64encbitbit64bootbroombslibcachemcheckmateclassclicliprclustercodetoolscolorspacecpp11crayondata.tabledigestdoParalleldplyre1071ellipseevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjomojquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMDSMapmemoisemgcvmicemimeminqamitmlmunsellnlmenloptrnnetnnlsnumDerivordinalpanpillarpkgconfigplotrixplyrpolynomprettyunitsprincurveprogressproxypurrrR6rappdirsRColorBrewerRcppRcppEigenreadrreshaperglrlangrmarkdownrpartrstudioapisassscalesshapesmacofstringistringrsurvivaltibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisviridisLitevroomweightswithrwordcloudxfunyaml

polymapR: linkage mapping in outcrossing polyploids

Peter M. Bourke, Geert van Geest

Rendered fromVignette_polymapR.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-06-01
Started: 2017-12-05

Using genotype probabilities in polymapR

Peter M. Bourke, Yanlin Liao

Rendered fromVignette_genotype_probabilities.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-01-09
Started: 2020-07-15

Readme and manuals

Help Manual

Help pageTopics
Add back duplicate markers after mappingadd_dup_markers
A dosage matrix for a random pairing tetraploid with five linkage groups.ALL_dosages screened_data screened_data2 screened_data3 segregating_data TRI_dosages
A (nested) list of linkage data frames classified per linkage group and homologueall_linkages_list_P1 all_linkages_list_P1_split all_linkages_list_P1_subset
Assign non-SN markers to a linkage group and homologue(s).assign_linkage_group
Assign (leftover) 1.0 markersassign_SN_SN
Use bridge markers to cluster homologues into linkage groupsassembleDuplexLinks bridgeHomologues
Build a list of segregation typescalcSegtypeInfo
Check the quality of a linkage mapcheck_map
Check for consistent marker assignment between both parentscheck_marker_assignment
check your dataset's maxP distributioncheck_maxP
Identify the best-fitting F1 segregation typescheckF1
Example output of the checkF1 functionchk1
Cluster 1.0 markers into correct homologues per linkage groupcluster_per_LG
Cluster 1.0 markerscluster_SN_markers
Compare linkage maps, showing links between connecting markers common to neighbouring mapscompare_maps
Consensus LG assignmentconsensus_LG_assignment
Find consensus linkage group namesconsensus_LG_names
Convert marker dosages to the basic types.convert_marker_dosages
Convert (probabilistic) genotype calling results from polyRAD to input compatible with polymapRconvert_polyRAD
Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.convert_updog
Check if dosage scores may have to be shiftedcorrectDosages
Create a phased homologue map list using the original dosagescreate_phased_maplist
Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrixcreateTetraOriginInput
Generate linkage group and homologue structure of SxN markersdefine_LG_structure
Example output dataset of polyRAD::PipelineMapping2Parents functionexampleRAD_mapping
Linkage analysis between all markertypes within a linkage group.finish_linkage_analysis
Visualize and get all markertype combinations for which there are functions in polymapRget_markertype_combinations
An example of a genotype probability data framegp_df
gp_overviewgp_overview
A list of objects needed to build the probabilistic genotype vignettegp_vignette_data
Assign markers to linkage groups and homologues.homologue_lg_assignment
A nested list with integrated mapsintegrated.maplist
A 'data.frame' specifying the assigned homologue and linkage group number per SxN markerLGHomDf_P1_1 LGHomDf_P2_1 LGHomDf_P2_2
Calculate recombination frequency, LOD and phaselinkage
Calculate recombination frequency, LOD and phase using genotype probabilitieslinkage.gp
A sample mapmap1
A sample mapmap2
A sample mapmap3
A list of maps of one parentmaplist_P1 maplist_P1_subset maplist_P2_subset
Perform binning of markers.marker_binning
Summarize marker datamarker_data_summary
Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimatesMDSMap_from_list
Merge homologuesmerge_homologues
Example output dataset of updog::multidog functionmout
Plotting 1.0 links between homologuesoverviewSNlinks
A list of cluster stacks at different LOD scoresP1_homologues P2_homologues P2_homologues_triploid
A 'data.frame' with marker assignmentsmarker_assignments_P1 marker_assignments_P2 P1_DxN_Assigned P1_SxS_Assigned P2_DxN_Assigned P2_SxS_Assigned P2_SxS_Assigned_2
Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploidp4_functions
Calculate frequency of each markertype.parental_quantities
Perform a PCA on progenyPCA_progeny
Phase 1.0 markers at the diploid levelphase_SN_diploid
A list of phased mapsphased.maplist
Plot homologue position versus integrated positionsplot_hom_vs_LG
Plot linkage mapsplot_map
Visualise the phased homologue maplistplot_phased_maplist
Plot r versus LODr_LOD_plot
Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.r2_1.0_1.0 r2_1.0_1.1 r2_1.1_1.1 r2_functions
Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.r3_2_1.0_1.0 r3_2_1.0_1.1 r3_2_1.0_1.2 r3_2_1.2_1.2 r3_functions
Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploidr4_functions
Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploidr6_functions
Screen for duplicate individualsscreen_for_duplicate_individuals
Screen for duplicate individuals using weighted genotype probabilitiesscreen_for_duplicate_individuals.gp
Screen for and remove duplicated markersscreen_for_duplicate_markers
Screen marker data for NA valuesscreen_for_NA_values
A linkage 'data.frame'.SN_DN_P1 SN_DN_P2 SN_SN_P1 SN_SN_P2 SN_SN_P2_triploid SN_SS_P1 SN_SS_P2
Identify deviations in LOD scores between pairs of simplex x nulliplex markersSNSN_LOD_deviations
Check for and estimate preferential pairingtest_prefpairing
Write out a nested listwrite_nested_list
Write pwd files from a nested listwrite_pwd_list
Write MapChart filewrite.mct
Write a JoinMap compatible .pwd file from linkage data.frame.write.pwd
Write TetraploidSNPMap input filewrite.TSNPM