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
onemap 2.0.6
(To be included)
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 2.0.8
Fixing chi-square segregation tests for markers with missing
classes
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 2.1.1002
onemap_read_vcfR function
Examples files for rils and backcross populations
Vignette for inbred and outcrossing updated
onemap 2.1.1003
rf_graph_table updated with ggplot2 and plotly
NAMESPACE automated with roxygen2
onemap 2.1.1004
write_onemap_raw function
onemap 2.1.1005
Vignette updated
onemap 2.1.1006
vcf2raw as defunct
onemap 2.1.1007
draw_map2 function
Vignette update
onemap 2.1.1008
mds_onemap function
Vignette update
onemap 2.1.2
Submitted to CRAN
onemap 2.1.2001
Adapt compare to rils and backcross
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 2.2.0
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 2.3.0
Remove functions to perform simulations
Remove updog and PedigreeSim dependency
Edit haplotypes graphics
onemap 2.4.0
Add testthat tests
Bug fix in functions
onemap 2.5.0
Add group_upgma function
onemap 2.6.0
HMM parallelization also available for Windows systems
Add simulated data for tests purpose
onemap 2.6.5
Removing MDSMap from dependencies
onemap 2.7.0
Updated vignettes
Github workflow
Include hmm=FALSE option for ordering algorithms
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 2.8.2
Replacing is by inherits to fix issues in R dev versions
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 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 3.2.0
Announce about MAPpoly included in the README
Fix “subscript out of bounds” warning while running rf_2pts
Update vignettes
Update tests
onemap 3.2.1
Fix c++ error in clang-ASAN and gcc-ASAN systems
onemap 3.2.2
Update citation
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
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