Genome_intervals-class(genomeIntervals)
Genome_intervals-class()所属R语言包：genomeIntervals
Class "Genome\_intervals"
类基因组\ _intervals“
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A set of genomic intervals without specified strand. Genomic intervals are intervals over the integers with two further annotations: seq_name (a chromosome or more generally a sequence of origin) and inter_base (logical) that states whether the interval is to be understood as an interval over bases
一套没有指定链的基因组间隔。基因组的时间间隔是与另外两个注解：在整数间隔seq_name（染色体或更普遍的原籍序列）和inter_base（logical），国家是否是可以理解的时间间隔作为一个间隔超过碱基
插槽----------Slots----------
.Data: See Intervals_full
.Data：见Intervals_full
annotation: A "data.frame" with the same number of rows as .Data. It has a column named seq_name that is a factor and does not contain missing values. seq_name is used to represent the chromosome or more generally the sequence of origin of the intervals. annotation has a column named inter_base that is logical and does not contain missing values. inter_base is FALSE if the interval is to be understood as an interval over bases (such as coding-sequence) and TRUE if it is over inter-bases (such as restriction site or an insertion position). Like base intervals, inter-base interval are encoded over the integers. An inter-base at position n indicates the space between base n and n+1.
annotation："data.frame"与相同数量的行.Data的。它名为seq_name这是一个因素，并且不包含缺失值的列。 seq_name用来表示染色体或更普遍的起源的时间间隔序列。 annotation有一列名为inter_base这是逻辑，并且不包含缺失值。 inter_base是FALSE如果间隔是要理解了碱基的时间间隔（如编码序列）和TRUE如果是多间碱基（如限制网站或插入的位置）。像基区间，基间间隔以上的整数编码。一个位置n间碱基表示碱基n和n+1之间的空间。
closed: See Intervals_full
closed：见Intervals_full
type: See Intervals_full
type：见Intervals_full
延伸----------Extends----------
Class "Intervals_full", directly. Class "Intervals_virtual", by class "Intervals\_full", distance 2. Class "matrix", by class "Intervals\_full", distance 3. Class "array", by class "Intervals\_full", distance 4. Class "structure", by class "Intervals\_full", distance 5. Class "vector", by class "Intervals\_full", distance 6, with explicit coerce.
类"Intervals_full"，直接。类"Intervals_virtual"，类“警告\ _full”，距离为2。类"matrix"“类”警告\ _full“，距离3。类"array"“类”警告\ _full“，距离4。类"structure"“类”警告\ _full“，距离5。类"vector"，类“警告\ _full”，距离6，具有明确的要挟。
方法----------Methods----------
[ signature(x = "Genome_intervals"): ...
[signature(x = "Genome_intervals")...
[[ signature(x = "Genome_intervals"): ...
[signature(x = "Genome_intervals")：...
[[<- signature(x = "Genome_intervals"): ...
[< - signature(x = "Genome_intervals")...
\$ signature(x = "Genome_intervals"): ...
\ $signature(x = "Genome_intervals")...
\$<- signature(x = "Genome_intervals"): ...
\ $ < - signature(x = "Genome_intervals")：...
annotation signature(object = "Genome_intervals"): ...
注释signature(object = "Genome_intervals")：...
annotation<- signature(object = "Genome_intervals"): ...
注释< - signature(object = "Genome_intervals")...
coerce signature(from = "Genome_intervals", to = "Intervals_full"): ...
要挟signature(from = "Genome_intervals", to = "Intervals_full")...
coerce signature(from = "Genome_intervals", to = "character"): ...
要挟signature(from = "Genome_intervals", to = "character")...
distance\_to\_nearest signature(from = "Genome_intervals", to = "Genome_intervals"): ...
距离\ _to \ _nearestsignature(from = "Genome_intervals", to = "Genome_intervals")...
inter\_base signature(x = "Genome_intervals"): ...
除\ _base signature(x = "Genome_intervals")：...
inter\_base<- signature(x = "Genome_intervals"): ...
除\ _base < - signature(x = "Genome_intervals")...
interval\_complement signature(x = "Genome_intervals"): ...
间隔\ _complementsignature(x = "Genome_intervals")...
interval\_intersection signature(x = "Genome_intervals"): ...
间隔\ _intersectionsignature(x = "Genome_intervals")...
interval\_overlap signature(from = "Genome_intervals", to = "Genome_intervals"): ...
间隔\ _overlapsignature(from = "Genome_intervals", to = "Genome_intervals")...
interval\_union signature(x = "Genome_intervals"): ...
区间\ _unionsignature(x = "Genome_intervals")...
seq\_name signature(x = "Genome_intervals"): ...
SEQ \ _name的signature(x = "Genome_intervals")：...
seq\_name<- signature(x = "Genome_intervals"): ...
SEQ \ _name的< - signature(x = "Genome_intervals")...
size signature(x = "Genome_intervals"): ...
大小signature(x = "Genome_intervals")：...
type<- signature(x = "Genome_intervals"): ...
类型< - signature(x = "Genome_intervals")...
注意----------Note----------
A Genome_intervals is a "Intervals_full" of type Z (i.e. a set of intervals over the integers). The annotation slot can carry further columns that can serve as annotations.
一个Genome_intervals"Intervals_full"的Z型（即一组间隔以上的整数）。 annotation插槽，可以进行进一步的列可以作为注释。
参见----------See Also----------
Genome_intervals_stranded for a derived class that allows stranded genomic intervals.
Genome_intervals_stranded派生类，允许滞留基因间隔。
举例----------Examples----------
# The "Genome_intervals" class[的“Genome_intervals”级]
i <- new(
"Genome_intervals",
matrix(
c(1,2,
3,5,
4,6,
8,9
),
byrow = TRUE,
ncol = 2
),
closed = matrix(
c(
TRUE, FALSE,
TRUE, FALSE,
TRUE, TRUE,
TRUE, FALSE
),
byrow = TRUE,
ncol = 2
),
annotation = data.frame(
seq_name = factor(c("chr01","chr01", "chr02","chr02")),
inter_base = c(FALSE, FALSE, TRUE, TRUE)
)
)
colnames(i) <- c( "start", "end" )
# print [打印]
print(i)
# size (number of bases per interval)[大小（每间隔碱基）]
size(i)
## simpler way to construct a Genome_intervals object:[＃简单的方法来构建一个Genome_intervals对象：]
G <- GenomeIntervals(start=c(1,3,4,5,8,10), end=c(5,5,6,8,9,11),
chromosome=rep(c("chr2","chrX","chr1"), each=2),
leftOpen=rep(c(FALSE, FALSE, TRUE), 2))
show(G)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 19:20:38
