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Updates #47

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b2fbd81
replace by inherits
Cristianetaniguti Nov 26, 2022
4539d42
remove ind update
Cristianetaniguti Nov 29, 2022
32eb5b0
building function #63
Cristianetaniguti Apr 23, 2023
54ff189
export QTLpoly input #64
Cristianetaniguti Apr 24, 2023
66eb1d8
Create plot_genome_vs_cm.R
jeekinlau Apr 24, 2023
b3c97de
add documentation roxygen
jeekinlau Apr 25, 2023
6cca1c4
update for one chromosome
jeekinlau Apr 25, 2023
43ff374
fixed kosambi and haldane and checks for sequence or list
jeekinlau Apr 26, 2023
522637a
Merge pull request #65 from jeekinlau/main
Cristianetaniguti Apr 26, 2023
be0a1f5
add summary_maps function
jeekinlau May 17, 2023
901556e
Merge branch 'main' of https://github.com/jeekinlau/onemap
jeekinlau May 17, 2023
3580e4a
rename to summary_maps_onemap
jeekinlau May 18, 2023
b9b959e
bugifx
Cristianetaniguti Jun 24, 2023
56d5f7c
bugifx
Cristianetaniguti Jun 26, 2023
ce5b665
Merge pull request #68 from Cristianetaniguti/main
Cristianetaniguti Jun 28, 2023
088c27a
edit cMxMb plot
Cristianetaniguti Jun 28, 2023
95f834c
adding test for #66
Cristianetaniguti Jun 28, 2023
e7a867c
Merge pull request #69 from Cristianetaniguti/improving
Cristianetaniguti Jun 28, 2023
6997725
Merge pull request #67 from jeekinlau/main
Cristianetaniguti Jun 28, 2023
5acac25
Merge pull request #70 from Cristianetaniguti/main
Cristianetaniguti Jun 28, 2023
1aaa544
function review #71
Cristianetaniguti Jun 28, 2023
7928a54
fix test
Cristianetaniguti Jun 28, 2023
1665d30
Merge pull request #72 from Cristianetaniguti/improving
Cristianetaniguti Jun 28, 2023
d9cd913
fix #73
Cristianetaniguti Jun 28, 2023
f9a232e
update actions version
Cristianetaniguti Jun 28, 2023
1ca3526
Merge pull request #74 from Cristianetaniguti/improving
Cristianetaniguti Jun 28, 2023
43ea933
fix #63
Cristianetaniguti Jun 29, 2023
65d8018
Merge pull request #75 from Cristianetaniguti/improving
Cristianetaniguti Jun 29, 2023
a933e80
fix #76
Cristianetaniguti Jun 30, 2023
71f3dcd
fix #64
Cristianetaniguti Jun 30, 2023
016df59
Merge pull request #77 from Cristianetaniguti/improving
Cristianetaniguti Jun 30, 2023
13f8a7d
fix #78
Cristianetaniguti Jun 30, 2023
bf7f7b8
update version
Cristianetaniguti Jun 30, 2023
699f539
fix #80
Cristianetaniguti Jun 30, 2023
5cc5379
more tests
Cristianetaniguti Jul 3, 2023
42c14ff
Merge pull request #81 from Cristianetaniguti/improving
Cristianetaniguti Jul 3, 2023
e3f95c3
bugfix read_mapmaker
Cristianetaniguti Aug 13, 2023
6cbe886
fix order edition
Cristianetaniguti Aug 28, 2023
7d6e863
Merge pull request #82 from Cristianetaniguti/improving
Cristianetaniguti Aug 29, 2023
32b5997
bugfix
Cristianetaniguti Aug 29, 2023
4898a0d
Merge pull request #83 from Cristianetaniguti/improving
Cristianetaniguti Aug 29, 2023
4e05a24
remove warnings
Cristianetaniguti Oct 16, 2023
c8ffc56
up version
Cristianetaniguti Oct 16, 2023
0669137
bugfix
Cristianetaniguti Oct 26, 2023
f72488d
up version
Cristianetaniguti Oct 26, 2023
d85ef3f
update paper
Cristianetaniguti Oct 27, 2023
15708c7
up vig
Cristianetaniguti Dec 27, 2023
2bad256
changing f2 C and D codification
Cristianetaniguti Oct 25, 2024
1fb5e89
change dominant codification
Cristianetaniguti Oct 25, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/check-standard.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ jobs:
steps:
- uses: actions/checkout@v2

- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}

Expand Down
10 changes: 6 additions & 4 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
Package: onemap
Title: Construction of Genetic Maps in Experimental Crosses
Version: 3.0.0
Version: 3.1.2
Description: 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.
Date: 2022-02-10
Authors@R: c(person("Gabriel",
"Margarido",
role = "aut",
Expand All @@ -26,6 +25,9 @@ Authors@R: c(person("Gabriel",
person("Rodrigo",
"Amadeu",
role = "ctb"),
person("Jeekin",
"Lau",
role = "ctb"),
person("Karl",
"Broman",
role = "ctb"),
Expand All @@ -43,7 +45,7 @@ Authors@R: c(person("Gabriel",
email = "[email protected]"))
Author: Gabriel Margarido [aut], Marcelo Mollinari [aut],
Cristiane Taniguti [ctb, cre], Getulio Ferreira [ctb],
Rodrigo Amadeu [ctb], Karl Broman [ctb],
Rodrigo Amadeu [ctb], Jeekin Lau [ctb], Karl Broman [ctb],
Katharine Preedy [ctb, cph] (MDS ordering algorithm),
Bastian Schiffthaler [ctb, cph] (HMM parallelization),
Augusto Garcia [aut, ctb]
Expand Down Expand Up @@ -84,5 +86,5 @@ Repository: CRAN
Packaged: 2019-09-22 22:25:43 UTC; cris
NeedsCompilation: yes
Date/Publication: 2019-09-22 22:48:07 UTC
RoxygenNote: 7.1.2
RoxygenNote: 7.2.3
biocViews:
9 changes: 9 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,11 @@ export(create_probs)
export(draw_map)
export(draw_map2)
export(drop_marker)
export(edit_order_onemap)
export(empty_onemap_obj)
export(est_map_hmm_out)
export(export_mappoly_genoprob)
export(export_viewpoly)
export(extract_depth)
export(filter_2pts_gaps)
export(filter_missing)
Expand All @@ -45,17 +48,20 @@ export(group_upgma)
export(haldane)
export(keep_only_selected_mks)
export(kosambi)
export(load_onemap_sequences)
export(make_seq)
export(map)
export(map_avoid_unlinked)
export(map_overlapping_batches)
export(marker_type)
export(mds_onemap)
export(onemap_read_vcfR)
export(ord_by_geno)
export(order_seq)
export(parents_haplotypes)
export(pick_batch_sizes)
export(plot_by_segreg_type)
export(plot_genome_vs_cm)
export(progeny_haplotypes)
export(progeny_haplotypes_counts)
export(rcd)
Expand All @@ -68,6 +74,7 @@ export(rf_graph_table)
export(rf_snp_filter_onemap)
export(ripple_seq)
export(rm_dupli_mks)
export(save_onemap_sequences)
export(seeded_map)
export(select_segreg)
export(seq_by_type)
Expand All @@ -77,6 +84,7 @@ export(sort_by_pos)
export(split_2pts)
export(split_onemap)
export(suggest_lod)
export(summary_maps_onemap)
export(test_segregation)
export(test_segregation_of_a_marker)
export(try_seq)
Expand All @@ -88,6 +96,7 @@ export(write_onemap_raw)
import(Rcpp)
import(dplyr)
import(ggplot2)
import(ggpubr)
import(graphics)
import(parallel)
import(princurve)
Expand Down
15 changes: 14 additions & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -171,4 +171,17 @@ Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Mollinari, M., Da, G., Pereira,
* 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
* 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: )
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