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:
polymapR_1.1.6.tar.gz
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polymapR.pdf |polymapR.html✨
polymapR/json (API)
# Install 'polymapR' in R: |
install.packages('polymapR', repos = c('https://pbourkey.r-universe.dev', 'https://cloud.r-project.org')) |
- ALL_dosages - A dosage matrix for a random pairing tetraploid with five linkage groups.
- LGHomDf_P1_1 - A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
- LGHomDf_P2_1 - A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
- LGHomDf_P2_2 - A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker
- P1_DxN_Assigned - A 'data.frame' with marker assignments
- P1_SxS_Assigned - A 'data.frame' with marker assignments
- P1_homologues - A list of cluster stacks at different LOD scores
- P2_DxN_Assigned - A 'data.frame' with marker assignments
- P2_SxS_Assigned - A 'data.frame' with marker assignments
- P2_SxS_Assigned_2 - A 'data.frame' with marker assignments
- P2_homologues - A list of cluster stacks at different LOD scores
- P2_homologues_triploid - A list of cluster stacks at different LOD scores
- SN_DN_P1 - A linkage 'data.frame'.
- SN_DN_P2 - A linkage 'data.frame'.
- SN_SN_P1 - A linkage 'data.frame'.
- SN_SN_P2 - A linkage 'data.frame'.
- SN_SN_P2_triploid - A linkage 'data.frame'.
- SN_SS_P1 - A linkage 'data.frame'.
- SN_SS_P2 - A linkage 'data.frame'.
- TRI_dosages - A dosage matrix for a random pairing tetraploid with five linkage groups.
- all_linkages_list_P1 - A (nested) list of linkage data frames classified per linkage group and homologue
- all_linkages_list_P1_split - A (nested) list of linkage data frames classified per linkage group and homologue
- all_linkages_list_P1_subset - A (nested) list of linkage data frames classified per linkage group and homologue
- chk1 - Example output of the checkF1 function
- exampleRAD_mapping - Example output dataset of polyRAD::PipelineMapping2Parents function
- gp_df - An example of a genotype probability data frame
- gp_vignette_data - A list of objects needed to build the probabilistic genotype vignette
- integrated.maplist - A nested list with integrated maps
- map1 - A sample map
- map2 - A sample map
- map3 - A sample map
- maplist_P1 - A list of maps of one parent
- maplist_P1_subset - A list of maps of one parent
- maplist_P2_subset - A list of maps of one parent
- marker_assignments_P1 - A 'data.frame' with marker assignments
- marker_assignments_P2 - A 'data.frame' with marker assignments
- mout - Example output dataset of updog::multidog function
- phased.maplist - A list of phased maps
- screened_data - A dosage matrix for a random pairing tetraploid with five linkage groups.
- screened_data2 - A dosage matrix for a random pairing tetraploid with five linkage groups.
- screened_data3 - A dosage matrix for a random pairing tetraploid with five linkage groups.
- segregating_data - A dosage matrix for a random pairing tetraploid with five linkage groups.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:2310636196. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 30 2024 |
R-4.5-win | OK | Aug 30 2024 |
R-4.5-linux | OK | Aug 30 2024 |
R-4.4-win | OK | Aug 30 2024 |
R-4.4-mac | OK | Aug 30 2024 |
R-4.3-win | OK | Aug 30 2024 |
R-4.3-mac | OK | Aug 30 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:abindbackportsbase64encbitbit64bootbroombslibcachemcandisccarcarDatacheckmateclassclicliprclustercodetoolscolorspacecowplotcpp11crayondata.tableDerivdigestdoBydoParalleldplyre1071ellipseevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenheplotshighrHmischmshtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjomojquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsMDSMapmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmunsellnlmenloptrnnetnnlsnumDerivordinalpanpbkrtestpillarpkgconfigplotrixplyrpolynomprettyunitsprincurveprogressproxypurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrreshaperglrlangrmarkdownrpartrstudioapisassscalesshapesmacofSparseMstringistringrsurvivaltibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisviridisLitevroomweightswithrwordcloudxfunyaml
polymapR: linkage mapping in outcrossing polyploids
Rendered fromVignette_polymapR.Rmd
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Rendered fromVignette_genotype_probabilities.Rmd
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