Updates

.github/workflows/check-standard.yaml

@@ -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 }}
 

DESCRIPTION

@@ -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",
@@ -26,6 +25,9 @@ Authors@R: c(person("Gabriel",
              person("Rodrigo", 
                     "Amadeu", 
                     role = "ctb"),
+             person("Jeekin", 
+                    "Lau", 
+                    role = "ctb"),
              person("Karl",
                     "Broman", 
                     role = "ctb"),
@@ -43,7 +45,7 @@ Authors@R: c(person("Gabriel",
                     email = "augusto.garcia@usp.br"))
 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]
@@ -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:

NAMESPACE

@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -88,6 +96,7 @@ export(write_onemap_raw)
 import(Rcpp)
 import(dplyr)
 import(ggplot2)
+import(ggpubr)
 import(graphics)
 import(parallel)
 import(princurve)

NEWS.md

@@ -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: )