-
Notifications
You must be signed in to change notification settings - Fork 26
/
NAMESPACE
124 lines (123 loc) · 3.38 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
# Generated by roxygen2: do not edit by hand
export(JaBbA)
export(Rcplex2)
export(read.junctions)
importFrom(DNAcopy,CNA)
importFrom(DNAcopy,segment)
importFrom(DNAcopy,smooth.CNA)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,match)
importFrom(GenomicRanges,setdiff)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,values)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,diag)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Matrix,which)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,readVcf)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(gGnome,balance)
importFrom(gGnome,gG)
importFrom(gTrack,gTrack)
importFrom(gUtils,"%$%")
importFrom(gUtils,"%&%")
importFrom(gUtils,"%Q%")
importFrom(gUtils,"%^%")
importFrom(gUtils,dt2gr)
importFrom(gUtils,gr.breaks)
importFrom(gUtils,gr.disjoin)
importFrom(gUtils,gr.dist)
importFrom(gUtils,gr.duplicated)
importFrom(gUtils,gr.end)
importFrom(gUtils,gr.findoverlaps)
importFrom(gUtils,gr.fix)
importFrom(gUtils,gr.flipstrand)
importFrom(gUtils,gr.in)
importFrom(gUtils,gr.match)
importFrom(gUtils,gr.nochr)
importFrom(gUtils,gr.quantile)
importFrom(gUtils,gr.rand)
importFrom(gUtils,gr.reduce)
importFrom(gUtils,gr.sample)
importFrom(gUtils,gr.setdiff)
importFrom(gUtils,gr.simplify)
importFrom(gUtils,gr.start)
importFrom(gUtils,gr.string)
importFrom(gUtils,gr.stripstrand)
importFrom(gUtils,gr.sum)
importFrom(gUtils,gr.tile)
importFrom(gUtils,gr.tile.map)
importFrom(gUtils,gr.val)
importFrom(gUtils,gr2dt)
importFrom(gUtils,grbind)
importFrom(gUtils,grl.bind)
importFrom(gUtils,grl.eval)
importFrom(gUtils,grl.in)
importFrom(gUtils,grl.pivot)
importFrom(gUtils,grl.unlist)
importFrom(gUtils,hg_seqlengths)
importFrom(gUtils,parse.gr)
importFrom(gUtils,ra.duplicated)
importFrom(gUtils,ra.overlaps)
importFrom(gUtils,rrbind)
importFrom(gUtils,seg2gr)
importFrom(gUtils,si2gr)
importFrom(gUtils,streduce)
importFrom(gplots,col2hex)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(graphics,title)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,clusters)
importFrom(igraph,graph)
importFrom(igraph,graph.adjacency)
importFrom(igraph,induced.subgraph)
importFrom(methods,as)
importFrom(methods,is)
importFrom(optparse,OptionParser)
importFrom(optparse,make_option)
importFrom(optparse,parse_args)
importFrom(optparse,print_help)
importFrom(parallel,mclapply)
importFrom(rtracklayer,import)
importFrom(sequenza,baf.model.fit)
importFrom(sequenza,get.ci)
importFrom(sequenza,segment.breaks)
importFrom(stats,C)
importFrom(stats,acf)
importFrom(stats,aggregate)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,ks.test)
importFrom(stats,lag)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,ppois)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(utils,read.delim)
importFrom(utils,write.table)
useDynLib(JaBbA)