SNPMaP-class(SNPMaP)
SNPMaP-class()所属R语言包：SNPMaP
Class SNPMaP
类SNPMaP
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A class of objects for SNP Microarrays and Pooling using Affymetrix arrays.
一类对象的SNP芯片技术和Pooling利用Affymetrix阵列。
用法----------Usage----------
## S4 method for signature 'SNPMaP'
as.matrix(x, mm=FALSE, ...)
## S4 method for signature 'SNPMaP,missing'
plot(x, FUN=function(x){x}, xlim=c(loX, hiX), ylim=c(0, hiY), xlab="guess",
ylab="Density", main="", col=rainbow(length(x@chps)),
legend.position="left", legend.bty="n", lty=1:length(x@chps),
zero.line=TRUE, ...)
## S4 method for signature 'SNPMaP'
boxplot(x, FUN=function(x){x}, ylab="guess", main="", ...)
## S4 method for signature 'SNPMaP'
image(x, chips=x@chps, prompt=FALSE, FUN=log, col=grey(seq(0,1,0.01)), fastRender=4,
rows=x@celDim[1], cols=x@celDim[2], ...)
参数----------Arguments----------
参数：x
object of class SNPMaP.
对象类SNPMaP。
参数：mm
logical indicating whether the data in the mismatch slot should be returned instead.
逻辑指示是否应该返回mismatch插槽中的数据，而不是。
参数：FUN
function specifying how each data point should be transformed before plotting. Try log for probe intensity data.
功能指定打印之前，每个数据点应该转变。尝试log探针强度数据的。
参数：xlim
the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a 'reversed axis'.
在x限制（X1，X2）的图。需要注意的是X1> X2是允许的，“扭转轴的。
参数：ylim
the y limits of the plot.
在y限制的图。
参数：xlab
character; a label for the x axis, defaults to a description of x.
字符x轴的标签，默认为x的描述。
参数：ylab
character; a label for the y axis, defaults to a description of y.
字符y轴的标签，默认的描述y的。
参数：main
character; a main title for the plot.
字符的主标题的图。
参数：col
the colours for the lines.
颜色的线条。
参数：legend.position
position of the legend in the pane to the right of the graph.
图右侧窗格中的传奇地位。
参数：legend.bty
the type of box to be drawn around the legend. The allowed values are "o" and "n".
“类型”框中周围绘制的传说。允许的值是“O”和“n”。
参数：lty
the line type.
线路类型。
参数：zero.line
logical; if TRUE, add a base line at y = 0
逻辑，如果为TRUE，在y = 0的基准线
参数：chips
character or numeric; the arrays to be imaged from the chps slot.
字符或数字阵列成像chps插槽。
参数：prompt
logical indicating whether the user should be asked before moving on to the next image.
逻辑指示用户是否应要求，然后再进入到下一个图像。
参数：fastRender
numeric n indicating 1/n rows and columns should be imaged.
数字N表示1 / n的行和列应该是imaged。
参数：rows
numeric; the number of rows of probes on the array.
数字;阵列上的探针的行的数目。
参数：cols
numeric; the number of columns of probes on the array.
数字;阵列上的探针的列的数目。
参数：...
additional arguments passed to methods.
额外的参数传递给方法。
插槽----------Slots----------
snpdata:Object of class SNPMaPdata, either a matrix or a FileDoubleMatrix with probe intensities or Relative Allele Score (RAS) estimates from the SNPMaP experiment.
snpdata：类的对象SNPMaPdata，无论是matrix或FileDoubleMatrix，与探针强度或相对等位基因分数的（RAS）估计从SNPMaP实验中。
mismatch:As snpdata. Contains mismatch probe intensities if they are present on the microarray and required for analysis.
mismatch：snpdata。包含错配探针强度，如果它们存在的微阵列上，并分析所需。
useMM:Object of class logical, if TRUE then the mismatch probe intensities will be subtracted from the perfect match probe intensities during the analysis. Defaults to FALSE.
useMM：类的对象logical，如果TRUE然后不匹配的探针强度将被减去的完美匹配探针强度在分析过程中。默认为FALSE的。
normalize:Object of class logical, if TRUE then the probe intensities will be quantile normalised across arrays during the analysis. Defaults to FALSE.
normalize：类的对象logical如果TRUE然后将探针强度将跨阵列在分析过程中位数归。默认为FALSE的。
logInt:Object of class logical, if TRUE then the raw probe intensities from the array will be replaced with the natural log of the intensities during the analysis. Defaults to FALSE.
logInt：类的对象logical如果TRUE然后从数组中的原始探针强度将被替换的强度，在分析过程中的自然对数。默认为FALSE的。
summary:Object of class function, the function that will be used to summarise the vector of RAS scores from all the quartets corresponding to a single SNP within an array into a single statistic per SNP per array. Should accept a numeric vector comprising doubles between 0 and 1 and NA and return a single value. Defaults to qcMean.
summary：类的对象function，将被用于所有的四重奏对应一个单一的数组内的SNP阵列，每SNP每到一个单一的统计总结矢量的RAS分数的功能。应该接受numeric向量，包括0和1之间和NA，并返回一个单一的值增加一倍。默认为qcMean的。
lowMemory:Object of class logical, if TRUE then the analysis will attempt to minimise the amount of RAM used by storing the snpdata and mismatch matricies as objects of class FileDoubleMatrix (see the link[R.huge:R.huge-package]{R.huge} package) on disk at the location named in the tempDir slot. Defaults to TRUE.
lowMemory：类的对象logical，如果TRUE那么分析将尝试为对象，以尽量减少由存储snpdata和mismatchmatricies的RAM使用类FileDoubleMatrix（参见link[R.huge:R.huge-package]{R.huge}包）命名tempDir插槽的位置在磁盘上。默认为TRUE的。
tempDir:Object of class character. Names the location of a writable directory where lowMemory versions of the snpdata and mismatch matricies may be stored. Defaults to '.' (ie the working directory).
tempDir：对象的类character。名称lowMemory版本的snpdata和mismatchmatricies存储的可写目录的位置。默认为。 （即工作目录）。
table:Object of class character. Gives the current format of the snpdata. May be (in order) 'empty', 'raw', 'long', 'short', 'ras' or 'rasS'.
table：对象的类character。给出格式的snpdata。可能是（按顺序），“空”，“原始”，“长”，“短”，“RAS”或“RASS”。
chiptype:Object of class character naming the type of array involved in this analysis ('Mapping250K\_Sty', for example). The arrays in a SNPMaP object must be of a single chiptype.
chiptype：类的对象character命名的类型，在本分析中所涉及的阵列（Mapping250K \ _Sty，例如）。在SNPMaP对象的数组必须是一个单一的chiptype。
celDim:Object of class numeric vector of two giving the number of rows and columns of probes on the chip. Read from the CEL header by cel2raw(), used for pseudo images of arrays.
celDim：对象的类numeric矢量的两个给探针在芯片上的行和列的数目。读取CEL头cel2raw()，用于伪images阵列。
set:Object of class numeric. Several of the Affymetrix chips have groups of probesets with different numbers of quartets. For example, the Mapping250K\_Sty array has probesets comprising 6 or 10 quartets. set specifies which group of probes are to be included in the current SNPMaP object. It defaults to 1, which corresponds to the largest group of probes on the array (ie those with 6 quartets on the Mapping250K\_Sty). Further groups can be accessed by setting set to 2 or higher. For more information, see SNPMaP.cdm-package.
set：对象的类numeric。的Affymetrix芯片中有几个具有不同数目的四重奏组probesets。例如，Mapping250K \ _Sty数组有probesets含有6个或10个四重奏。 set指定，探针组是包含在目前的SNPMaP对象。它的默认值为1，对应于最大的一组探测器阵列上（即那些与6上的Mapping250K \ _Sty四重奏）。通过设置set为2或更高，进一步的基团可以被访问。欲了解更多信息，请参阅SNPMaP.cdm-package。
snps:Object of class character. A vector of the SNPs being analysed in the current SNPMaP object.
snps：对象的类character。一个向量的SNP分析，在当前的的SNPMaP对象。
chps:Object of class character. A vector of the CEL files in the current analysis. Defaults to all the files ending '.CEL' in the working directory.
chps：对象的类character。当前分析中的CEL文件的向量。默认的所有文件结束“。CEL”的工作目录。
cols:Object of class character. A vector identifying the columns of the snpdata and mismatch slots of the current SNPMaP object.
cols：对象的类character。一个矢量确定snpdata和mismatch插槽，目前的SNPMaP对象的列。
width:Object of class numeric. The number of quartets per SNP in the current group of probesets.
width：对象的类numeric。当前组中的probesets四重奏每个SNP的数目。
transformation:Object of class character. A vector to record transformations carried out on the data.
transformation：对象的类character。一个向量，记录转换的数据。
experiment:Object of class factor. A factor identifying the experimental group each array belongs to. Not used at present.
experiment：对象的类factor。实验组每个阵列的一个因素确定归属。目前未使用。
annotation:Object of class list. A slot to hold annotation to be used in the analysis. Not used at present.
annotation：对象的类list。一个插槽持有注解中使用的分析。目前未使用。
created:Object of class character; the date and time when this SNPMaP object was created.
created：类的对象character;时的日期和时间这个SNPMaP对象被创建。
version:Object of class character; the version number of the SNPMaP package that created this object.
version：对象的类character; SNPMaP包创建此对象的版本号。
majorHistory:Object of class list. A record of the major functions carried out on this SNPMaP object, along with the date and time they were called.
majorHistory：对象的类list。 A记录的主要功能进行了这SNPMaP对象，连同日期和时间，他们被称为。
方法----------Methods----------
as.matrixsignature(x="SNPMaP"): returns the contents of the snpdata slot as a matrix, or, if mm=TRUE, returns the contents of the mismatch slot.
as.matrix signature(x="SNPMaP")：返回的内容snpdata插槽，一个matrix，或者，如果mm=TRUE，返回的内容mismatch插槽。
plotsignature(x="SNPMaP", y="missing"): plots the density of the contents of the snpdata slot, with each array represented by a single line identified in a legend. Uses layout.
图signature(x="SNPMaP", y="missing")：图density的snpdata插槽，每个数组在图例中确定的由一个单一的线代表的内容。使用layout。
boxplotsignature(x="SNPMaP"): box plot for each array in the snpdata slot.
箱线图signature(x="SNPMaP")：snpdata插槽中为每个阵列箱线图。
imagesignature(x="SNPMaP"): if the object is in 'raw' format, draws a pseudo image of the array as it was scanned to check for artefacts.
图像signature(x="SNPMaP")：如果对象是在“原始”形式，得出的数组，因为它是一个伪图像扫描，以检查是否有文物。
opensignature(con="SNPMaP"): if the data in the SNPMaP object is stored on disk, open a connection.
打开signature(con="SNPMaP")：如果SNPMaP对象存储在磁盘上，打开一个连接中的数据。
closesignature(con="SNPMaP"): if the data is on disk, close the connection.
密切signature(con="SNPMaP")：如果是在磁盘上的数据，关闭连接。
summarysignature(object="SNPMaP"): summary of the SNPMaP object.
总结signature(object="SNPMaP")：总结SNPMaP对象。
[signature(x="SNPMaP", i="missing", j="missing"): Extract subsets of the data contained in the snpdata slot of the SNPMaP object. Using a single index ([] rather than [,]) returns rows.
[signature(x="SNPMaP", i="missing", j="missing")：snpdata插槽SNPMaP对象中包含的数据提取的子集。使用一个单一的指数（[]而不是[,]）返回行。
[signature(x="SNPMaP", i="ANY", j="missing"): see above.
[signature(x="SNPMaP", i="ANY", j="missing")：见上面。
[signature(x="SNPMaP", i="missing", j="ANY"): see above.
[signature(x="SNPMaP", i="missing", j="ANY")：见上面。
[signature(x="SNPMaP", i="ANY", j="ANY"): see above.
[signature(x="SNPMaP", i="ANY", j="ANY")：见上面。
initializesignature(.Object="SNPMaP"): default initialize method.
初始化signature(.Object="SNPMaP")：默认初始化方法。
参见----------See Also----------
SNPMaP-package.<br> SNPMaP.cdm-package.<br> snpmap() to set up a SNPMaP analysis.<br> disk2memory() to transfer SNPMaP objects between disk and memory.<br> cel2ras() for workflow functions.<br> cloneSNPMaP() to copy a SNPMaP object on disk.<br> writeSNPMaP() to write SNPMaP objects to text files.
SNPMaP-package。<BR> SNPMaP.cdm-package。<BR>的snpmap()设置了一个SNPMaP的分析。<BR>disk2memory()转移SNPMaP磁盘和内存之间的对象。<BR> cel2ras()工作流功能。<BR> cloneSNPMaP()复制一个SNPMaP对象在磁盘上的。<BR> writeSNPMaP()写SNPMaP对象文本文件。
实例----------Examples----------
## Not run: [＃不运行：]
## Getting started[＃入门]
## Creates the 'raw' SNPMaP object x on disk with mismatch probes included[＃创建“原始”SNPMaP对象x磁盘上的错配探针]
x<-snpmap(useMM=TRUE, RUN='cel2raw', lowMemory=TRUE)
## Print a summary of the SNPMaP object[打印摘要的SNPMaP对象的]
summary(x)
## Add a comment (prints in the summary)[＃添加评论（打印摘要）]
comment(x)<-'High and low extreme pools from January'
## View pseudo image to screen for artefacts[＃查看屏幕文物的假象]
image(x)
## Plot probe intensities[＃图探针强度]
plot(x, FUN=log)
boxplot(x, FUN=log)
## tidy=TRUE removes the FileDoubleMatrix from the old x to keep the disk tidy[＃整齐= TRUE消除了从旧的X FileDoubleMatrix保持磁盘整洁]
x<-raw2ras(x, tidy=TRUE)
## Plot Relative Allele Scores[＃图相对等位基因成绩的]
plot(x)
## Default tidy=FALSE does not remove the original FileDoubleMatrix from disk[＃默认整齐= FALSE不从磁盘上删除原来的FileDoubleMatrix]
## Useful if you want to keep x (no side effects)[＃有用的，如果你想保持X（无副作用）]
y<-ras2rasS(x)
## View the first ten rows[＃查看前十行]
as.matrix(y[1:10,])
## View a set of SNPs[＃查看一组的单核苷酸多态性]
as.matrix(y[c("SNP_A-4192909", "SNP_A-4192918"),])
## Transfer the SNPMaP object from disk to memory[从磁盘到内存】＃转移的SNPMaP的的对象]
y<-disk2memory(y, tidy=TRUE)
## Run the analysis again from CEL files to RAS summaries without viewing intermediate stages[＃再次运行分析CEL文件的的RAS摘要不观看的中间阶段]
## This time in memory (may require a lot of RAM)[＃这个时候在内存中（可能需要大量的RAM）]
z<-snpmap(useMM=TRUE, RUN='cel2rasS', lowMemory=FALSE)
plot(z)
## Get the RAS summary scores as a standard matrix[＃取得RAS总结成绩作为标准矩阵]
rasSummaries<-as.matrix(z)
## Read all the sets into a list[＃读取到一个列表中的所有套]
allSets<-msnpmap(set=0)
## End(Not run)[＃（不执行）]
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 2012-9-30 11:11:53
