NEWS

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onemap 3.2.5

• Bugfix: map_avoid_unlinked for f2 backcross was searching for unexisting genotype
• Bugfix: onemap_read_vcfR codification for A.2 markers

onemap 3.2.4

• This version better address package citation
• Removes rebus dependency
• Removes deprecated R_ext/PrtUtil.h usage
• Change maintainer email
• Update authors order
• Removing statgen.ncsu.edu unavailable server from docs

onemap 3.2.2

• Update citation

onemap 3.2.1

• Fix c++ error in clang-ASAN and gcc-ASAN systems

onemap 3.2.0

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

onemap 3.1.0

• 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 interactive edition of ordering (edit_order_onemap)
• 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 :smile: )

onemap 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 result by increasing the tolerance value
• Fix bug in mds_onemap

onemap 2.8.2

• Replacing is by inherits to fix issues in R dev versions

onemap 2.8.0

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

onemap 2.7.0

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

onemap 2.6.5

• Removing MDSMap from dependencies

onemap 2.6.0

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

onemap 2.5.0

• Add group_upgma function

onemap 2.4.0

• Add testthat tests
• Bug fix in functions

onemap 2.3.0

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

onemap 2.2.0

• split_onemap function to split onemap objects
• filter_missing function to filter markers in onemap object by missing data
• map parallelized with Batchmap method
• Option rm_unlinked in map to remove markers which not reach the linkage criterias when estimating genetic distances by HMM
• All ordering algorithms now presents the possibility to parallelize the last step (map) and remove automatically unlinked markers and repeat the ordering procedure
• suggest_lod function now works also with sequence objects
• Remove argument hmm from mds_onemap
• Solve numerical problems with small negative LOD values in rf_2pts
• Update all RDatas to new format and compressed form
• Function map_avoid_unlinked to automatically remove the unlinked markers and restart the map
• create_depths_profile plots allele counts and genotypes from vcf, onemap and errors
• runpedsim wrapper function for PedigreeSim software
• pedsim2raw converts PedigreeSim outputs to onemap raw file
• pedsim2vcf converts PedigreeSim outputs to VCF file simulating counts with updog or negative binomial
• Replace all get() by nothing
• Export parents and progeny haplotypes with write_haplotypes.R
• Draw graphics for progeny haplotypes
• F2 intercross populations now uses the same HMM than outcrossing populations. Modification needed to correct infer dominant markers and also to export progeny haplotypes.
• Function vcf2progeny_haplotypes to convert phased VCF in onemap_progeny_haplotypes object. It make possible to draw the haplotypes for phased VCFs.
• Function seq_by_type split sequence by marker type
• Internal function map_save_ram creates new onemap object for only the evaluated sequence and, after finished process that require too much RAM memory, it return the complete onemap object to user. This save RAM memory in parallelization process.
• Vignettes update
• Documentation update

onemap 2.1.2001

• Adapt compare to rils and backcross

onemap 2.1.1008

• mds_onemap function
• Vignette update

onemap 2.1.1007

• draw_map2 function
• Vignette update

onemap 2.1.1006

• vcf2raw as defunct

onemap 2.1.1005

• Vignette updated

onemap 2.1.1004

• write_onemap_raw function

onemap 2.1.1003

• rf_graph_table updated with ggplot2 and plotly
• NAMESPACE automated with roxygen2

onemap 2.1.1002

• onemap_read_vcfR function
• Examples files for rils and backcross populations
• Vignette for inbred and outcrossing updated

onemap 2.1.1001

• Bug fix in function test_segregation for F2 cross
• Fix in example f2
• Codif_data changed to deal with dominant markers for F2
• Warnings removed and labels added to outcross plot
• plot.onemap palette changed
• Included C.A, D.B and A.H.B types in plot by segregation
• New argument in select_segreg
• Function create_data_bins now keeps CHROM and POS infos
• Possible to make sequences from CHROM and POS using 2pts object
• Outcrossing vcf example file are available
• New functions group_seq and print.group_seq
• Functions draw.try and draw_order are now defuncts
• Vignette for outcrossing updated
• F2 vcf example file are available
• Vignette for inbred updated

onemap 2.1.3

• draw_map2 now receives data.frames
• Changing class functions to is
• Adapt try_seq to rils and backcross
• onemap_read_vcfR also accept phased VCF
• Submitted to CRAN

onemap 2.1.2

• Submitted to CRAN

onemap 2.0.8

• Fixing chi-square segregation tests for markers with missing classes

onemap 2.0.7

• Updating .travis.yml for the newer standards
• Updating README in order to solve Windows user's issues.
• Updating dependencies and NAMESPACE for newer standards (R-3.4.0)
• Updating dependencies within Bioconductor packages

onemap 2.0.6

• (To be included)

onemap 2.0.5

• Organizing the files in directories to allow installation from github
• Moving functions descriptions for roxygen style
• Solving conflict of version 2.0.4 with 2.0.5 (the one in CRAN)
• Replacing old vignettes in pdf with new ones using RMarkdown
• Adding functions to plot raw data
• Adding functions to draw graphics showing marker categories
• Adding functions to perform chi-square tests for marker segregation
• Adding functions to identify alpha under Bonferroni's argument
• Correcting documentation not compiling for RMarkdown
• Updating dependencies for other R packages