Package: onemap 3.0.0

Cristiane Taniguti

onemap: Construction of Genetic Maps in Experimental Crosses

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.

Authors:Gabriel Margarido [aut], Marcelo Mollinari [aut], Cristiane Taniguti [ctb, cre], Getulio Ferreira [ctb], Rodrigo Amadeu [ctb], Karl Broman [ctb], Katharine Preedy [ctb, cph], Bastian Schiffthaler [ctb, cph], Augusto Garcia [aut, ctb]

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onemap.pdf |onemap.html✨
onemap/json (API)

# Install 'onemap' in R:
install.packages('onemap', repos = c('https://augusto-garcia.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/augusto-garcia/onemap/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • LG3_comp - Dataset needed for build Outcrossing vignette. It is the result from compare function exemplified there.
  • mapmaker_example_f2 - Simulated data from a F2 population
  • onemap_example_bc - Simulated data from a backcross population
  • onemap_example_f2 - Simulated data from a F2 population
  • onemap_example_out - Data from a full-sib family derived from two outbred parents
  • onemap_example_riself - Simulated data from a RIL population produced by selfing.
  • simu_example_bc - Simulated data from a backcross population
  • simu_example_f2 - Simulated data from a f2 intercross population
  • simu_example_out - Simulated data from a outcrossing population
  • vcf_example_bc - Data generated from VCF file with biallelic markers from a f2 backcross population
  • vcf_example_f2 - Data generated from VCF file with biallelic markers from a f2 intercross population
  • vcf_example_out - Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents
  • vcf_example_riself - Data generated from VCF file with biallelic markers from a RIL population produced by selfing

On CRAN:

8.87 score 35 stars 170 scripts 403 downloads 7 mentions 66 exports 159 dependencies

Last updated 2 years agofrom:d71d3c4800. Checks:OK: 4 ERROR: 2 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64NOTENov 02 2024
R-4.5-linux-x86_64OKNov 02 2024
R-4.4-win-x86_64NOTENov 02 2024
R-4.4-mac-x86_64OKNov 02 2024
R-4.4-mac-aarch64ERRORNov 02 2024
R-4.3-win-x86_64NOTENov 02 2024
R-4.3-mac-x86_64OKNov 02 2024
R-4.3-mac-aarch64ERRORNov 02 2024

Exports:add_markeradd_redundantsBonferroni_alphacheck_datacheck_twoptscombine_onemapcomparecreate_data_binscreate_depths_profilecreate_probsdraw_mapdraw_map2drop_markerempty_onemap_objest_map_hmm_outextract_depthfilter_2pts_gapsfilter_missingfilter_probfind_binsgroupgroup_seqgroup_upgmahaldanekeep_only_selected_mkskosambimake_seqmapmap_avoid_unlinkedmap_overlapping_batchesmarker_typemds_onemaponemap_read_vcfRorder_seqparents_haplotypespick_batch_sizesplot_by_segreg_typeprogeny_haplotypesprogeny_haplotypes_countsrcdread_mapmakerread_onemaprecordremove_indsrf_2ptsrf_graph_tablerf_snp_filter_onemapripple_seqrm_dupli_mksseeded_mapselect_segregseq_by_typeseriationset_map_funsort_by_possplit_2ptssplit_onemapsuggest_lodtest_segregationtest_segregation_of_a_markertry_seqtry_seq_by_sequgvcf2rawwrite_mapwrite_onemap_raw

Dependencies:abindapeaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDatacheckmateclassclicliprclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextendDerivdigestdoBydoParalleldplyre1071ellipseevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2ggpubrggrepelggsciggsignifglmnetgluegridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjomojquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisememusemgcvmicemicrobenchmarkmimeminqamitmlmodelrmunsellnlmenloptrnnetnnlsnumDerivopensslordinalpanpbkrtestpermutepillarpinfsc50pkgconfigplotlyplotrixplyrpolynomprettyunitsprincurveprogresspromisesproxypurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrrebusrebus.baserebus.datetimesrebus.numbersrebus.unicodereshape2rlangrmarkdownrpartrstatixrstudioapisassscalesshapesmacofSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytextzdbucminfutf8vcfRvctrsveganviridisviridisLitevroomweightswithrwordcloudxfunyaml

Inbred Based Populations

Statistical Genetics Lab Department of Genetics Luiz de Queiroz College of Agriculture University of São Paulo

Rendered fromInbred_Based_Populations.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2022-11-21
Started: 2015-04-19

Introduction to R

Statistical Genetics Lab Department of Genetics Luiz de Queiroz College of Agriculture University of São Paulo

Rendered fromIntroduction_R.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2022-11-21
Started: 2015-03-23

Outcrossing Populations

Statistical Genetics Lab Department of Genetics Luiz de Queiroz College of Agriculture University of São Paulo

Rendered fromOutcrossing_Populations.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2022-11-21
Started: 2015-07-27

Overview

Statistical Genetics Lab Department of Genetics Luiz de Queiroz College of Agriculture University of São Paulo

Rendered fromOverview.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2022-11-21
Started: 2015-03-22

Readme and manuals

Help Manual

Help pageTopics
Perform gaussian sumacum
Creates a new sequence by adding markers.add_marker
Add the redundant markers removed by create_data_bins functionadd_redundants
Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)Bonferroni_alpha
Onemap object sanity checkcheck_data
Twopts object sanity checkcheck_twopts
Combine OneMap datasetscombine_onemap
Compare all possible orders (exhaustive search) for a given sequence of markerscompare
New dataset based on binscreate_data_bins
Create a dataframe suitable for a ggplot2 graphiccreate_dataframe_for_plot_outcross
Create database and ggplot graphic of allele reads depthscreate_depths_profile
Build genotype probabilities matrix for hmmcreate_probs
Draw a genetic mapdraw_map
Draw a linkage mapdraw_map2
Creates a new sequence by dropping markers.drop_marker
Produce empty object to avoid code break. Function for internal purpose.empty_onemap_obj
Extract allele counts of progeny and parents of vcf fileextract_depth
Filter markers based on 2pts distancefilter_2pts_gaps
Filter markers according with a missing data thresholdfilter_missing
Function filter genotypes by genotype probabilityfilter_prob
Allocate markers into binsfind_bins
Function to divide the sequence in batches with user defined sizegenerate_overlapping_batches
Assign markers to linkage groupsgroup
Assign markers to preexisting linkage groupsgroup_seq
Assign markers to linkage groupsgroup_upgma
Apply Haldane mapping functionhaldane
Keep in the onemap and twopts object only markers in the sequenceskeep_only_selected_mks
Apply Kosambi mapping functionkosambi
Dataset needed for build Outcrossing vignette. It is the result from compare function exemplified there.LG3_comp
Create a sequence of markers based on other OneMap object typesmake_seq
Construct the linkage map for a sequence of markersmap
Repeat HMM if map find unlinked markermap_avoid_unlinked
Mapping overlapping batchesmap_overlapping_batches
Perform map using background objects with only selected markers. It saves ram memory during the procedure. It is useful if dealing with many markers in total data set.map_save_ram
Simulated data from a F2 populationmapmaker_example_f2
Informs the segregation patterns of markersmarker_type
OneMap interface with MDSMap package with option for multipoint distances estimationmds_onemap
Simulated data from a backcross populationonemap_example_bc
Simulated data from a F2 populationonemap_example_f2
Data from a full-sib family derived from two outbred parentsonemap_example_out
Simulated data from a RIL population produced by selfing.onemap_example_riself
Convert vcf file to onemap objectonemap_read_vcfR
Search for the best order of markers combining compare and try_seq functionsorder_seq
Generates data.frame with parents estimated haplotypesparents_haplotypes
Picking optimal batch size valuespick_batch_sizes
Draw a graphic showing the number of markers of each segregation pattern.plot_by_segreg_type
Draw a graphic of raw data for any OneMap populationplot.onemap
Plots progeny haplotypesplot.onemap_progeny_haplotypes
Plot recombination breakpoints counts for each individualplot.onemap_progeny_haplotypes_counts
Plot p-values for chi-square tests of expected segregationplot.onemap_segreg_test
print method for object class 'compare'print.compare
Print method for object class 'onemap'print.onemap
print method for object class 'onemap_bin'print.onemap_bin
Show the results of segregation testsprint.onemap_segreg_test
Print order_seq objectprint.order
Print method for object class 'sequence'print.sequence
Generate data.frame with genotypes estimated by HMM and its probabilitiesprogeny_haplotypes
Plot number of breakpoints by individualsprogeny_haplotypes_counts
Rapid Chain Delineationrcd
Read data from a Mapmaker raw fileread_mapmaker
Read data from all types of progenies supported by OneMapread_onemap
Recombination Counting and Orderingrecord
Remove individuals from the onemap objectremove_inds
Two-point analysis between genetic markersrf_2pts
Plots pairwise recombination fractions and LOD Scores in a heatmaprf_graph_table
Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.rf_snp_filter_onemap
Compares and displays plausible alternative orders for a given linkage groupripple_seq
Remove duplicated markers keeping the one with less missing datarm_dupli_mks
Construct the linkage map for a sequence of markers after seeding phasesseeded_map
Show markers with/without segregation distortionselect_segreg
Extract marker number by nameseq_by_type
Seriationseriation
Defines the default mapping functionset_map_fun
Simulated data from a backcross populationsimu_example_bc
Simulated data from a f2 intercross populationsimu_example_f2
Simulated data from a outcrossing populationsimu_example_out
Sort markers in onemap object by their position in reference genomesort_by_pos
Split rf_2pts object by markerssplit_2pts
Split onemap data setssplit_onemap
Suggests a LOD Score for two point testssuggest_lod
test_segregationtest_segregation
test_segregation_of_a_markertest_segregation_of_a_marker
Try to map a marker into every possible position between markers in a given maptry_seq
Run try_seq considering previous sequencetry_seq_by_seq
Unidirectional Growthug
Data generated from VCF file with biallelic markers from a f2 backcross populationvcf_example_bc
Data generated from VCF file with biallelic markers from a f2 intercross populationvcf_example_f2
Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parentsvcf_example_out
Data generated from VCF file with biallelic markers from a RIL population produced by selfingvcf_example_riself
These functions are defunct and no longer available.vcf2raw
Write a genetic map to a filewrite_map
Convert onemap object to onemap raw filewrite_onemap_raw