Snapshot-class(ShortRead)
Snapshot-class()所属R语言包：ShortRead
Class "Snapshot"
类“快照”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A Snapshot-class to visualize genomic data from BAM files with zoom and pan functionalities.
一个Snapshot一流的基因组数据的可视化与缩放和平移功能，BAM文件。
用法----------Usage----------
Snapshot(files, range, ...)
参数----------Arguments----------
参数：files
A character() or BamFileList specifying the file(s) to be visualized.
一个字符（）或BamFileList指定的文件（S）的可视化。
参数：range
A GRanges object specifing the range to be visualized.
一个GRangesspecifing对象的范围，可视化。
参数：...
Additional, optional, arguments to be passed to the Snapshot initialize function. Arguments include:
另外，可选，参数被传递快照initialize函数。参数包括：
functions:A SnapshotFunctionList of functions, in addition to built-in "fine_coverage", "coarse_coverage", "multifine_coverage", to be used for visualization.
功能：一SnapshotFunctionList的功能，除了内置的“fine_coverage，coarse_coverage，multifine_coverage，使用可视化。
currentFunction:character(1) naming the function, from functinos to be used for data input and visualization. The default chooses a function based on the scale at which the data is being visualized.
currentFunction：字符（1）命名的功能，从functinos被用于数据输入和可视化。默认选择基于规模的数据可视化功能。
annTrack:Annotation track. If built-in visulization functions are to be used, annTrack should be a GRanges instance and the first column of its elementMeatdata would be used to annotate the range.
annTrack：诠释轨道。如果要使用内置的visulization功能，annTrack应该是GRanges实例和其elementMeatdata的第一列将用来注释的范围。
fac:Character(1) indicating which factor used for grouping the sample files. The factor should be included in the elementMetadata of files, otherwise ignored. Used only to visualize multiple files.
因素：性格（1）哪些因素分组示例文件。的因素应包括在fileselementMetadata，否则忽略。仅用于可视化多个文件。
.auto_display:logical(1) indicating whether the visualization is to be updated when show is invoked.
。逻辑auto_display：（1）表示，是否要更新时show调用可视化。
.debuglogical(1) indicating whether debug messages are to be printed.
。debuglogical（1）说明是否要打印调试消息。
方法----------Methods----------
zoom signature(x = "Snapshot"): Zoom (in or out) the
变焦signature(x = "Snapshot")：放大（或缩小）
pan signature(x = "Snapshot"): Pan (right or left)
泛signature(x = "Snapshot")：潘（左或右）
togglefun signature(x = "Snapshot"): Toggle the current functions which imported records are to be immediately evaluated. Note that the active range will be changed to the
togglefunsignature(x = "Snapshot")：切换进口记录将被立即评估目前的职能。请注意，活动范围将改为
togglep signature(x = "Snapshot"): Toggle the panning
togglepsignature(x = "Snapshot")：切换平移
togglez signature(x = "Snapshot"): Toggle the zooming
togglezsignature(x = "Snapshot")：切换缩放
存取----------Accessors----------
show signature(object = "Snapshot"): Display a
显示signature(object = "Snapshot")：显示
files signature(x = "Snapshot"): Get the files
文件signature(x = "Snapshot")：files
functions signature(x = "Snapshot"): Get the functions field (object of SnapshotFunctionList) of a
功能signature(x = "Snapshot")：functions场（SnapshotFunctionList对象）的
view signature(x = "Snapshot"): Get the view
查看signature(x = "Snapshot")：view
vrange signature(x = "Snapshot"): Get the .range field (object of GRanges) of a Snapshot
vrangesignature(x = "Snapshot")：.range场（对象GRanges）Snapshot
getTrellis signature(x = "Snapshot"): Get the
getTrellissignature(x = "Snapshot")：获取
领域----------Fields----------
.debug: Object of class function to display
.debug：Object类的function显示
.auto_display: Object of class logical to
类的对象.auto_display：logical
.range: Object of class GRanges indicating
.range：Object类的GRanges说明
.zin: Object of class logical indicating
.zin：Object类的logical说明
.pright: Object of class logical indicating
.pright：Object类的logical说明
.data: Object of class data.frame containing
.data：Object类的data.frame包含
.data_dirty: Object of class logical
.data_dirty类logical：对象
.initial_functions: Object of class
.initial_functions：对象类
.current_function: Object of class character of the function the imported recored are currently evaluated and
.current_function：character类对象的功能导入条记录目前正在评估，并
annTrack: Default to NULL if not intended to visulize the annotation track. If default visulization function(s) is intended to be used to plot the annotation,
annTrack：默认为NULL如果不打算以visulize注解轨道。如果的默认visulization功能（S）的目的是要用来绘制批注，
functions: Object of class SnapshotFunctionList of customized functions to evaluate
functions类SnapshotFunctionList定制功能的对象，以评估
files: Object of class BamFileList to be imported.
files：Object类的BamFileList要依赖进口。
view: Object of class SpTrellis that is
view：Object类的SpTrellis这是
基于类的方法----------Class-Based Methods----------
display(): Display the current Snapshot object.
display()：显示当前的Snapshot对象。
pan(): Pan (right or left) the current plot.
pan()：潘（左或右）目前的图。
zoom(): Zoom (in or out) the current plot.
zoom()：放大（或缩小）当前的图。
toggle(zoom, pan, currentFunction): Toggle zooming, panning effects or the currentFuction in which the imported
toggle(zoom, pan, currentFunction)：切换缩放，平移的影响，其中进口currentFuction
作者（S）----------Author(s)----------
Martin Morgan and Chao-Jen Wong <a href="mailto:cwon2@fhcrc.org">cwon2@fhcrc.org</a>
参见----------See Also----------
SpTrellis
SpTrellis
举例----------Examples----------
## example 1: Importing specific ranges of records[＃示例1：导入记录的具体范围]
file <- system.file("extdata", "SRR002051.chrI-V.bam",
package="yeastNagalakshmi")
which <- GRanges("chrI", IRanges(1, 2e5))
s <- Snapshot(file, range=which)
## methods[＃方法]
zoom(s) # zoom in[放大]
## zoom in to a specific region[＃放大到一个特定的区域]
zoom(s, range=GRanges("chrI", IRanges(7e4, 7e4+8000)))
pan(s) # pan right[潘权]
togglez(s) # change effect of zooming[改变缩放效果]
zoom(s) # zoom out[缩小]
togglep(s) # chage effect of panning[CHAGE效果的平移]
pan(s)
## accessors[＃存取]
functions(s)
vrange(s)
show(s)
ignore.strand(s)
view(s) ## extract the spTrellis object[＃提取spTrellis对象。]
getTrellis(s) ## extract the trellis object[＃提取网格对象。]
## example 2: ignore strand[例2：忽略链]
s <- Snapshot(file, range=which, ignore.strand=TRUE)
##[＃]
## example 3: visulizing annotation track[＃示例3：visulizing注释轨道]
##[＃]
library(GenomicFeatures)
getAnnGR <- function(txdb, which) {
ex <- exonsBy(txdb, by="gene")
sn <- keepSeqlevels(ex, seqlevels(which))
r <- range(sn)
gr <- unlist(r)
values(gr)[["gene_id"]] <- rep.int(names(r), times=elementLengths(r))
gr
}
txdbFile <- system.file("extdata", "sacCer2_sgdGene.sqlite",
package="yeastNagalakshmi")
# txdb <- makeTranscriptDbFromUCSC(genome="sacCer2",[txdb < - makeTranscriptDbFromUCSC（基因组“sacCer2”]
# tablename="sgdGene")[TableName的=“sgdGene”）]
txdb <- loadFeatures(txdbFile)
which <- GRanges("chrI", IRanges(1, 2e5))
gr <- getAnnGR(txdb, which)
## note that the first column of the elementMetadata annotates of the[＃注意，第一列的elementMetadata的诠释]
## range of the elements.[＃范围内的元素。]
gr
s <- Snapshot(file, range=which, annTrack=gr)
annTrack(s)
## zoom in to an interesting region[＃放大到一个有趣的区域]
zoom(s, range=GRanges("chrI", IRanges(7e4, 7e4+8000)))
togglez(s) ## zoom out[＃放大了]
zoom(s)
pan(s)
## example 4, 5, 6: muliple BAM files with 'multicoarse_covarage'[＃示例4，5，6：muliple的BAM文件“multicoarse_covarage”]
## and 'mutifine_coverage' view.[＃和“mutifine_coverage的意见。]
## Resolution does not automatically switch for views of multiple[＃决议不自动切换多个视图]
## files. It is important to note if width(which) < 10,000, use[＃文件。重要的是要注意，如果宽度（）<10,000，使用]
## multifine_coverage. Otherwise use multicoarse_coverage[＃multifine_coverage。否则使用multicoarse_coverage]
file <- system.file("extdata", "SRR002051.chrI-V.bam",
package="yeastNagalakshmi")
which <- GRanges("chrI", IRanges(1, 2e5))
s <- Snapshot(c(file, file), range=which,
currentFunction="multicoarse_coverage")
## grouping files and view by 'multicoarse_coverage'[＃分组multicoarse_coverage的文件，并查看]
bfiles <- BamFileList(c(file, file))
values(bfiles) <- DataFrame(sampleGroup=factor(c("normal", "tumor")))
values(bfiles)
s <- Snapshot(bfiles, range=which,
currentFunction="multicoarse_coverage", fac="sampleGroup")
## grouping files and view by 'multifine_coverage'[＃分组multifine_coverage的文件，并查看]
which <- GRanges("chrI", IRanges(7e4, 7e4+8000))
s <- Snapshot(bfiles, range=which,
currentFunction="multifine_coverage", fac="sampleGroup")
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。
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发表于 2012-2-26 14:08:06
