/
NAMESPACE
69 lines (68 loc) · 1.83 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
# Generated by roxygen2: do not edit by hand
S3method(print,mipanalyzer_biallelic)
S3method(print,mipanalyzer_multiallelic)
S3method(summary,mipanalyzer_biallelic)
S3method(summary,mipanalyzer_multiallelic)
export(Pf_chrom_lengths)
export(check_MIPanalyzer_loaded)
export(explore_filter_coverage_loci)
export(explore_filter_coverage_samples)
export(filter_counts)
export(filter_coverage_loci)
export(filter_coverage_samples)
export(filter_loci)
export(filter_loci_invariant)
export(filter_overcounts)
export(filter_samples)
export(filter_wsaf)
export(get_IBS_distance)
export(get_IB_mixture)
export(get_genomic_distance)
export(get_spatial_distance)
export(get_wsaf)
export(inbreeding_mle)
export(is.mipanalyzer_biallelic)
export(is.mipanalyzer_multiallelic)
export(lonlat_to_bearing)
export(mipanalyzer_biallelic_to_vcfR)
export(mipanalyzer_file)
export(pca_wsaf)
export(pcoa_genomic_distance)
export(plot_coverage)
export(plot_distance)
export(plot_map)
export(plot_pca)
export(plot_pca_contribution)
export(plot_pca_variance)
export(plot_pcoa)
export(plot_wsaf)
export(rbetabinom)
export(rdirichlet)
export(sim_biallelic)
export(vcf_to_mipanalyzer_biallelic)
export(vcf_to_mipanalyzer_multiallelic)
import(ggplot2)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rcpp,sourceCpp)
importFrom(ape,pcoa)
importFrom(coda,geweke.diag)
importFrom(coda,mcmc)
importFrom(data.table,fread)
importFrom(grDevices,grey)
importFrom(methods,is)
importFrom(methods,new)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(rworldmap,getMap)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,rbeta)
importFrom(stats,rbinom)
importFrom(stats,rgamma)
importFrom(stats,runif)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
useDynLib(MIPanalyzer, .registration = TRUE)