/
NAMESPACE
155 lines (154 loc) · 3.84 KB
/
NAMESPACE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
# Generated by roxygen2: do not edit by hand
S3method(plot,group.upgma)
S3method(plot,onemap)
S3method(plot,onemap.pcmap)
S3method(plot,onemap.pcmap3d)
S3method(plot,onemap.spheremap)
S3method(plot,onemap_progeny_haplotypes)
S3method(plot,onemap_progeny_haplotypes_counts)
S3method(plot,onemap_segreg_test)
S3method(print,compare)
S3method(print,group)
S3method(print,group.upgma)
S3method(print,group_seq)
S3method(print,onemap)
S3method(print,onemap_bin)
S3method(print,onemap_segreg_test)
S3method(print,order)
S3method(print,rf_2pts)
S3method(print,sequence)
S3method(print,try)
export(Bonferroni_alpha)
export(add_marker)
export(add_redundants)
export(check_data)
export(check_twopts)
export(combine_onemap)
export(compare)
export(create_data_bins)
export(create_depths_profile)
export(create_probs)
export(draw_map)
export(draw_map2)
export(drop_marker)
export(empty_onemap_obj)
export(est_map_hmm_out)
export(extract_depth)
export(filter_2pts_gaps)
export(filter_missing)
export(filter_prob)
export(find_bins)
export(group)
export(group_seq)
export(group_upgma)
export(haldane)
export(keep_only_selected_mks)
export(kosambi)
export(make_seq)
export(map)
export(map_avoid_unlinked)
export(map_overlapping_batches)
export(marker_type)
export(mds_onemap)
export(onemap_read_vcfR)
export(order_seq)
export(parents_haplotypes)
export(pick_batch_sizes)
export(plot_by_segreg_type)
export(progeny_haplotypes)
export(progeny_haplotypes_counts)
export(rcd)
export(read_mapmaker)
export(read_onemap)
export(record)
export(remove_inds)
export(rf_2pts)
export(rf_graph_table)
export(rf_snp_filter_onemap)
export(ripple_seq)
export(rm_dupli_mks)
export(seeded_map)
export(select_segreg)
export(seq_by_type)
export(seriation)
export(set_map_fun)
export(sort_by_pos)
export(split_2pts)
export(split_onemap)
export(suggest_lod)
export(test_segregation)
export(test_segregation_of_a_marker)
export(try_seq)
export(try_seq_by_seq)
export(ug)
export(vcf2raw)
export(write_map)
export(write_onemap_raw)
import(Rcpp)
import(dplyr)
import(ggplot2)
import(graphics)
import(parallel)
import(princurve)
import(smacof)
import(tidyr)
importFrom(RColorBrewer,brewer.pal)
importFrom(dendextend,color_branches)
importFrom(ggpubr,ggarrange)
importFrom(grDevices,bmp)
importFrom(grDevices,colorRamp)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,jpeg)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,postscript)
importFrom(grDevices,rainbow)
importFrom(grDevices,tiff)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,pie)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(htmlwidgets,saveWidget)
importFrom(methods,is)
importFrom(plotly,ggplotly)
importFrom(rebus,number_range)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,chisq.test)
importFrom(stats,cor.test)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,predict)
importFrom(stats,qchisq)
importFrom(stats,quantile)
importFrom(stats,rect.hclust)
importFrom(stats,relevel)
importFrom(stats,rf)
importFrom(stats,setNames)
importFrom(utils,browseURL)
importFrom(utils,flush.console)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
importFrom(vcfR,extract.gt)
importFrom(vcfR,masplit)
importFrom(vcfR,read.vcfR)
useDynLib(onemap)