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polymapR  

Linkage Analysis in Outcrossing Polyploids
View on CRAN: Click here


Download and install polymapR package within the R console
Install from CRAN:
install.packages("polymapR")

Install from Github:
library("remotes")
install_github("cran/polymapR")

Install by package version:
library("remotes")
install_version("polymapR", "1.1.5")



Attach the package and use:
library("polymapR")
Maintained by
Peter Bourke
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-12-05
Latest Update: 2023-03-13
Description:
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) . Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) .
How to cite:
Peter Bourke (2017). polymapR: Linkage Analysis in Outcrossing Polyploids. R package version 1.1.5, https://cran.r-project.org/web/packages/polymapR
Previous versions and publish date:
1.0.11 (2017-12-05 19:39), 1.0.12 (2017-12-14 13:32), 1.0.13 (2018-02-13 19:07), 1.0.14 (2018-03-27 21:05), 1.0.15 (2018-04-13 11:04), 1.0.16 (2018-04-13 13:15), 1.0.17 (2018-08-24 16:30), 1.0.18 (2018-11-01 23:20), 1.0.19 (2019-02-01 16:00), 1.0.20 (2019-12-12 23:00), 1.1.0 (2020-07-16 00:30), 1.1.1 (2020-12-17 18:10), 1.1.2 (2021-03-09 16:20), 1.1.3 (2023-03-13 18:20), 1.1.4 (2023-11-04 20:10)
Other packages that cited polymapR R package
View polymapR citation profile
Other R packages that polymapR depends, imports, suggests or enhances
Functions, R codes and Examples using the polymapR R package
Some associated functions: ALL_dosages . LGHomDf_P1_1 . MDSMap_from_list . P1_SxS_Assigned . P1_homologues . PCA_progeny . SNSN_LOD_deviations . SN_SN_P1 . add_dup_markers . all_linkages_list_P1 . assign_SN_SN . assign_linkage_group . bridgeHomologues . calcSegtypeInfo . checkF1 . check_map . check_marker_assignment . check_maxP . chk1 . cluster_SN_markers . cluster_per_LG . compare_maps . consensus_LG_assignment . consensus_LG_names . convert_marker_dosages . convert_polyRAD . convert_updog . correctDosages . createTetraOriginInput . create_phased_maplist . define_LG_structure . exampleRAD_mapping . finish_linkage_analysis . get_markertype_combinations . gp_df . gp_overview . gp_vignette_data . homologue_lg_assignment . integrated.maplist . linkage.gp . linkage . map1 . map2 . map3 . maplist_P1 . marker_binning . marker_data_summary . merge_homologues . mout . overviewSNlinks . p4_functions . parental_quantities . phase_SN_diploid . phased.maplist . plot_hom_vs_LG . plot_map . plot_phased_maplist . polymapR-package . r2_functions . r3_functions . r4_functions . r6_functions . r_LOD_plot . screen_for_NA_values . screen_for_duplicate_individuals.gp . screen_for_duplicate_individuals . screen_for_duplicate_markers . test_prefpairing . write.TSNPM . write.mct . write.pwd . write_nested_list . write_pwd_list . 
Some associated R codes: aiding_functions.R . exported_functions.R . p4_functions.R . polymapR-package.R . r2_functions.R . r3_functions.R . r4_functions.R . r6_functions.R . roxygen_datasets.R .  Full polymapR package functions and examples
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