-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathNAMESPACE
104 lines (91 loc) · 2.6 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
## ============================================================
## Import
## ============================================================
# Import all packages listed as Imports or Depends
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### base packages
###
import(grid)
import(grDevices, except = 'windows')
import(utils)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Non-bioconductor packages
###
importFrom("psych",corr.test)
importFrom("colortools",complementary, opposite)
importFrom("gridExtra",arrangeGrob, grid.arrange)
importClassesFrom("hash",hash)
#importMethodsFrom("hash",keys)
importFrom("hash",hash)
importFrom("hash",has.key)
importFrom("stats",cor)
importFrom("corrplot",corrplot)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Bioconductor packages
###
import(IRanges)
import(S4Vectors)
import(GenomicRanges)
import(biomaRt)
import(Gviz)
import(rtracklayer)
## ============================================================
## Export
## ============================================================
# Export all names
#exportPattern("^[[:alpha:]]+")
#exportPattern("^[^\\.]")
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Primary functions
###
export(comet,comet.web,comet.list)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### pre-formatted tracks
###
export(chrUCSC2ENSEMBL,
gcContent_UCSC,
GWAScatalog_UCSC,
GAD_UCSC,
GeneReviews_UCSC,
refGenes_UCSC,
xenorefGenes_UCSC,
knownGenes_UCSC,
genesName_ENSEMBL,
genes_ENSEMBL,
interestGenes_ENSEMBL,
transcript_ENSEMBL,
interestTranscript_ENSEMBL,
snpBiomart_ENSEMBL,
snpLocations_UCSC,
structureBiomart_ENSEMBL,
ClinVarCnv_UCSC, ClinVarMain_UCSC,
CoreillCNV_UCSC,
COSMIC_UCSC,
cpgIslands_UCSC,
regulationBiomart_ENSEMBL,
bindingMotifsBiomart_ENSEMBL,
regulatorySegmentsBiomart_ENSEMBL,
regulatoryFeaturesBiomart_ENSEMBL,
otherRegulatoryRegionsBiomart_ENSEMBL,
regulatoryEvidenceBiomart_ENSEMBL,
miRNATargetRegionsBiomart_ENSEMBL,
repeatMasker_UCSC,
segmentalDups_UCSC,
chromHMM_RoadMap,
DNaseI_RoadMap,
dgfootprints_RoadMap,
eQTL_GTEx,
imprintedGenes_GTEx,
psiQTL_GTEx,
metQTL,eQTL,
TFBS_FANTOM,
DNaseI_FANTOM,
ChIPTF_ENCODE,
chromatinHMMAll_UCSC, chromatinHMMOne_UCSC,
HistoneAll_UCSC, HistoneOne_UCSC,
HiCdata2matrix)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### obselete tracks
###
#ISCATrack
# DNAse_UCSC,