SAM-class(siggenes)
SAM-class()所属R语言包：siggenes
Class SAM
类的SAM
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is a class representation for several versions of the SAM (Significance Analysis of Microarrays) procedure proposed by Tusher
这是一个类表示几个版本由Tusher提出的SAM（微阵列技术分析的意义）过程
类的对象----------Objects from the Class----------
Objects can be created using the functions sam, sam.dstat, sam.wilc and sam.snp.
创建对象可以使用的功能sam，sam.dstat，sam.wilc和sam.snp。
插槽----------Slots----------
d: Object of class "numeric" representing the
d：Object类的"numeric"代表
d.bar: Object of class "numeric" representing
d.bar：Object类的"numeric"代表
vec.false: Object of class "numeric" containing
vec.false：Object类的"numeric"包含
p.value: Object of class "numeric" consisting of
p.value：Object类的"numeric"组成
s: Object of class "numeric" representing the standard deviations of the genes. If the standard deviations are
s：Object类的"numeric"代表的基因的标准偏差。如果标准偏差
s0: Object of class "numeric" representing the value of the fudge factor. If not computed, s0 will be
s0：Object类的"numeric"代表的软糖因素的价值。如果不计算，s0会
mat.samp: Object of class "matrix" containing the permuted group labels used in the estimation of the null distribution. Each row represents one permutation, each column one observation (pair). If no permutation procedure has been used,
mat.samp：Object类的"matrix"含有置换组在空分布的估计使用的标签。每一行代表一个排列，每列一个观察（对）。如果没有置换的程序已被使用，
p0: Object of class "numeric" representing the
p0：Object类的"numeric"代表
mat.fdr: Object of class "matrix" containing general information as the number of significant genes and the estimated FDR for several values of Delta. Each row represents one
mat.fdr：Object类的"matrix"包含若干重要基因和Delta几个值估计FDR的一般信息。每一行代表一个
q.value: Object of class "numeric" consisting of the q-values of the genes. If not computed, q.value will be
q.value类"numeric" Q-值的基因组成的对象。如果不计算，q.value会
fold: Object of class "numeric" representing the fold changes of the genes. If not computed, fold will be
fold：Object类的"numeric"代表倍的基因变化。如果不计算，fold会
msg: Object of class "character" containing information about, e.g., the type of analysis. msg is printed when the functions
msg类"character"包含的信息，例如，类型的分析对象。 msg打印功能时
chip: Object of class "character" naming the microarray used in the analysis. If no information about the chip is available,
chip：Object类的"character"命名在分析中使用的芯片。如果没有提供有关芯片的信息是，
方法----------Methods----------
identify signature(x = "SAM"): After generating a SAM plot, identify can be used to obtain information about the genes by clicking on the symbols in the SAM plot. For details, see
确定signature(x = "SAM")：产生一个SAM图后，identify可以用来获得有关基因的信息，按一下在SAM图的符号。有关详情，请参阅
plot signature(x = "SAM"): Generates a SAM plot or the Delta plots. If the specified delta in plot(object,delta) is a numeric value, a SAM plot will be generated. If delta is either not specified or a numeric vector, the Delta plots will be generated. For details, see ?sam.plot2, ?delta.plot or
图signature(x = "SAM")：生成一个SAM图或Delta图。如果指定deltaplot(object,delta)是一个数值，SAM图将产生的。如果delta或者未指定或数字向量，Delta图将会产生。有关详细信息，请参阅?sam.plot2，?delta.plot
print signature(x = "SAM"): Prints general information such as the number of significant genes and the estimated FDR for a set of Delta. For details, see help.sam(print). Arguments are
打印signature(x = "SAM")：打印的一般信息，如若干重要基因，并估计了一套DeltaFDR。有关详细信息，请参阅help.sam(print)。论据
show signature(object = "SAM"): Shows the output of the SAM
显示signature(object = "SAM")：显示输出的SAM
summary signature(object = "SAM"): Summarizes the results of a SAM analysis. If delta in summary(object,delta) is not specified or a numeric vector, the information shown by print and some additional information will be shown. If delta is a numeric vector, the general information for the specific Delta is shown and additionally gene-specific information about the genes called significant using this value of Delta. The output of summary is an object of class sumSAM which has the slots row.sig.genes, mat.fdr, mat.sig and list.args. For details,
摘要signature(object = "SAM")：总结的SAM分析的结果。如果deltasummary(object,delta)未指定或数字向量，印刷和一些额外的信息中显示的信息将显示。 delta如果是一个数值向量，一般为具体的Delta信息显示，此外，特定的基因有关的基因的信息称为显着使用这个值的Delta。总结的输出是一个类sumSAM的对象，其中有插槽row.sig.genes，mat.fdr，mat.sig和list.args。有关详细信息，
注意----------Note----------
SAM was developed by Tusher et al. (2001).
萨姆被由Tusher等。 （2001年）。
!!! There is a patent pending for the SAM technology at Stanford University. !!!
！是为在斯坦福大学的SAM技术申请专利。 ！
作者（S）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schw@gmx.de">holger.schw@gmx.de</a>
参考文献----------References----------
the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany. http://www.sfb475.uni-dortmund.de/berichte/tr44-03.pdf.
Categorical Data – SAM and PAM for SNPs. To appear in: Proceedings of the the 28th Annual Conference of the GfKl.
applied to the ionizing radiation response. PNAS, 98, 5116-5121.
参见----------See Also----------
sam,args.sam,sam.plot2, delta.plot
sam，args.sam，sam.plot2，delta.plot
举例----------Examples----------
# Load the package multtest and the data of Golub et al. (1999)[加载的的包multtest和Golub等数据。 （1999）]
# contained in multtest.[载在multtest。]
library(multtest)
data(golub)
# Perform a SAM analysis for the two class unpaired case assuming[执行两个类未成的假设情况下的SAM分析]
# unequal variances.[异方差。]
sam.out <- sam(golub, golub.cl, B=100, rand=123)
sam.out
# Alternative ways to show the output of sam.[替代的方式来显示输出山姆。]
show(sam.out)
print(sam.out)
# Obtain a little bit more information.[获得多一点的信息。]
summary(sam.out)
# Print the results of the SAM analysis for other values of Delta.[打印Delta的其他值的SAM分析的结果。]
print(sam.out, seq(.2, 2, .2))
# Again, the same with additional information.[再次，与其他信息一样。]
summary(sam.out, seq(.2, 2, .2))
# Obtain the Delta plots for the default set of Deltas.[获得默认设置为DeltaDelta图。]
plot(sam.out)
# Generate the Delta plots for Delta = 0.2, 0.4, 0.6, ..., 2.[生成Delta= 0.2，0.4，0.6，...，2Delta图。]
plot(sam.out, seq(0.2, 0.4, 2))
# Obtain the SAM plot for Delta = 2.[获得SAMDelta= 2图。]
plot(sam.out, 2)
# Get information about the genes called significant using [获取信息有关的基因被称为显著使用]
# Delta = 3.[Delta= 3。]
sam.sum3 <- summary(sam.out, 3)
sam.sum3
# Obtain the rows of the Golub et al. (1999) data set containing[Golub等获得的行。 （1999年）的数据集，其中包含]
# the genes called differentially expressed[称为差异表达的基因]
sam.sum3@row.sig.genes
# and their names[他们的名字]
golub.gnames[sam.sum3@row.sig.genes, 3]
# The matrix containing the d-values, q-values etc. of the[含有D-值的矩阵，Q值等。]
# differentially expressed genes can be obtained by[可以通过以下方式获得差异表达基因]
sam.sum3@mat.sig
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 14:14:44
