OneMap version 3.2.0

• Announce about MAPpoly included in the README and load message
• Fix "subscript out of bounds" warning while running rf_2pts
• Update vignettes
• Update tests

OneMap version 3.1.0

• New preprint version describing modifications in OneMap:
  Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847

• New plot for cM x Mb relation (plot_genome_vs_cm)

• New function to export to VIEWpoly (export_viewpoly)

• New function to order markers by chromosome position (ord_by_geno)

• New function to create map summary (summary_maps_onemap) - based on MAPpoly function

• New function to an interactive edition of ordering (edit_order_onemap) - based on MAPpoly function

• New function to export haplotype probabilities to QTLpoly (export_mappoly_genoprob)

• Keep reference and alternative alleles information from imported VCF

• Return parents haplotypes using reference and alternative alleles codification when outcross or f2 cross type

• Functions to export and import reduced-size onemap R objects (save_onemap_sequences and load_onemap_sequences)

• Add new author (Jeekin Lau 😄 )

OneMap version 3.0.0

• New preprint including OneMap updates:

Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Mollinari, M., Da, G., Pereira, S., Riera-Lizarazu, O., Lau, J., Byrne, D., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., &; Franco Garcia, A. A. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847

• Functions to filter markers based on two-points estimations: filter_2pts_gaps and rf_snp_filter_onemap
• Optimization of find_bins and map_avoid_unlinked
• New function to save RAM memory after filters: keep_only_selected_mks
• Review spell_check
• Avoid -Inf likelihood resulted by increasing the tolerance value
• Fix bug in mds_onemap

v2.8.0000

• Updated vignettes
• Add parallelization.type argument to user choose between PSOCK and FORK
• vcfR as import
• remove unlist of rf_2pts

v2.7.0000

• Updated vignettes
• Github workflow
• Include hmm=FALSE option for ordering algorithms

v2.6.5000

• Removing MDSMap from dependencies

v2.6.0000

• HMM parallelization also available for Windows systems
• Add simulated data for tests purpose

v2.5.0000

• Add group_upgma function

v2.4.0000

• Add testthat tests
• Bug fix in functions

v2.3.0000

• Remove functions to perform simulations
• Remove updog and PedigreeSim dependency
• Edit haplotypes graphics