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
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
|
\name{VariantType-class}
\docType{class}
% Class
\alias{VariantType-class}
% Subclasses
\alias{CodingVariants-class}
\alias{IntronVariants-class}
\alias{FiveUTRVariants-class}
\alias{ThreeUTRVariants-class}
\alias{SpliceSiteVariants-class}
\alias{IntergenicVariants-class}
\alias{PromoterVariants-class}
\alias{AllVariants-class}
% Constructors for subclasses :
\alias{CodingVariants}
\alias{IntronVariants}
\alias{FiveUTRVariants}
\alias{ThreeUTRVariants}
\alias{SpliceSiteVariants}
\alias{IntergenicVariants}
\alias{PromoterVariants}
\alias{AllVariants}
% accessors :
\alias{upstream}
\alias{upstream,AllVariants-method}
\alias{upstream,PromoterVariants-method}
\alias{upstream,IntergenicVariants-method}
\alias{upstream<-}
\alias{upstream<-,AllVariants-method}
\alias{upstream<-,PromoterVariants-method}
\alias{upstream<-,IntergenicVariants-method}
\alias{idType}
\alias{idType<-}
\alias{idType,IntergenicVariants-method}
\alias{idType<-,IntergenicVariants-method}
\alias{downstream}
\alias{downstream,AllVariants-method}
\alias{downstream,PromoterVariants-method}
\alias{downstream,IntergenicVariants-method}
\alias{downstream<-}
\alias{downstream<-,AllVariants-method}
\alias{downstream<-,PromoterVariants-method}
\alias{downstream<-,IntergenicVariants-method}
\alias{promoter}
\alias{promoter,AllVariants-method}
\alias{promoter<-}
\alias{promoter<-,AllVariants-method}
\alias{intergenic}
\alias{intergenic,AllVariants-method}
\alias{intergenic<-}
\alias{intergenic<-,AllVariants-method}
% show method:
\alias{show,VariantType-method}
\alias{show,AllVariants-method}
\alias{show,PromoterVariants-method}
\title{VariantType subclasses}
\description{
\code{VariantType} subclasses specify the type of variant to be located with
\code{locateVariants}.
}
\usage{
CodingVariants()
IntronVariants()
FiveUTRVariants()
ThreeUTRVariants()
SpliceSiteVariants()
IntergenicVariants(upstream = 1e+06L, downstream = 1e+06L,
idType=c("gene", "tx"))
PromoterVariants(upstream = 2000L, downstream = 200L)
AllVariants(promoter = PromoterVariants(),
intergenic = IntergenicVariants())
}
\details{
\code{VariantType} is a virtual class inherited by the \code{CodingVariants},
\code{IntronVariants}, \code{FiveUTRVariants}, \code{ThreeUTRVariants},
\code{SpliceSiteVariants}, \code{IntergenicVariants} and \code{AllVariants}
subclasses.
The subclasses are used as the \code{region} argument to
\code{locateVariants}. They designate the type of variant (i.e., region of
the annotation to match) when calling \code{locateVariants}.
The majority of subclasses have no slots and require no arguments for an
instance to be created. \code{PromoterVariants} and \code{IntergenicVariants}
and accept \code{upstream} and \code{downstream} arguments that define
the number of base pairs upstream from the 5'-end and downstream from
the 3'-end of the transcript region. See the ?\code{locateVariants} man
page for details. \code{IntergenicVariants} also accepts a
\code{idType} that controls what IDs are returned in the
PRECEDEID and FOLLOWID metadata columns.
\code{AllVariants} accepts \code{promoter} and
\code{intergenic} arguments which are \code{PromoterVariants()} and
\code{IntergenicVariants()} objects with the appropriate
\code{upstream} and \code{downstream} values.
}
\arguments{
\item{upstream, downstream}{
Single \code{integer} values representing the number of base pairs
upstream of the 5'-end and downstream of the 3'-end. Used in contructing
\code{PromoterVariants()} and \code{IntergenicVariants()} objects only.
}
\item{idType}{
\code{character} indicating if the ids in the PRECEDEID and FOLLOWID
metadata columns should be gene ids ("gene") or transcript ids ("tx").
Applicable to \code{IntergenicVariants()} objects only.
}
\item{promoter}{
\code{PromoterVariants} object with appropriate \code{upstream} and
\code{downstream} values. Used when constructing \code{AllVariants}
objects only.
}
\item{intergenic}{
\code{IntergenicVariants} object with appropriate \code{upstream} and
\code{downstream} values. Used when constructing \code{AllVariants}
objects only.
}
}
\section{Accessors}{
In the following code, \code{x} is a \code{PromoterVariants} or a
\code{AllVariants} object.
\describe{
\item{}{
\code{upstream(x)}, \code{upstream(x) <- value}:
Gets or sets the number of base pairs defining a range
upstream of the 5' end (excludes 5' start value).
}
\item{}{
\code{downstream(x)}, \code{downstream(x) <- value}:
Gets or sets the number of base pairs defining a range
downstream of the 3' end (excludes 3' end value).
}
\item{}{
\code{idType(x)}, \code{idType(x) <- value}:
Gets or sets the \code{character()} which controls the id returned
in the PRECEDEID and FOLLOWID output columns. Possible values are
"gene" and "tx".
}
\item{}{
\code{promoters(x)}, \code{promoters(x) <- value}:
Gets or sets the \code{PromoterVariants} in the
\code{AllVariants} object.
}
\item{}{
\code{intergenic(x)}, \code{intergenic(x) <- value}:
Gets or sets the \code{IntergenicVariants} in the
\code{AllVariants} object.
}
}
}
\author{Valerie Obenchain}
\seealso{
\itemize{
\item The promoters function on the
\link[GenomicRanges]{intra-range-methods} man page in the
GenomicRanges package.
}
}
\examples{
CodingVariants()
SpliceSiteVariants()
PromoterVariants(upstream=1000, downstream=10000)
## Default values for PromoterVariants and IntergenicVariants
AllVariants()
## Modify 'upstream' and 'downstream' for IntergenicVariants
AllVariants(intergenic=IntergenicVariants(500, 100))
## Reset PromoterVariants on existing AllVariants object
av <- AllVariants()
av
promoter(av) <- PromoterVariants(100, 50)
av
}
|
