R语言 SPIAssay包 SPIAssay()函数中文帮助文档(中英文对照)

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SPIAssay(SPIAssay)
SPIAssay()所属R语言包：SPIAssay

                                        A genetic-based assay for the identification of cell lines
                                         的遗传基础的检测的单元系的鉴定

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The SNP Panel Identification Assay (SPIA) is a package that enables an  accurate determination of cell line identity from the genotype of single nucleotide  polymorphisms (SNPs). The SPIA test allows to discern when two cell lines are close  enough to be called similar and when they are not.
SNP面板标识含量（SPIA），是一个软件包，可以准确测定单元株的身份从单核苷酸多态性（SNP）位点的基因型。 SPIA测试可以辨别两种单元株的距离足够近时，当他们被称为类似。


Details

详细信息----------Details----------

</table>
</ TABLE>

The most important function of the package is SPIATest that computes SPIA distance on a set of cell lines and perform the associated probabilistic test. Another important function is  SPIAPlot that creates a summary graph of the SPIA test. Finally, toSPIAData function encodes generic representations of genotype calls into a format compatible with SPIA.
包的函数是最重要的SPIATest，计算SPIA距离上一组单元株，并进行相关的概率测试。另一个重要的功能是SPIAPlot创建一个概要图的SPIA测试的。最后，toSPIAData函数通用的基因型来电表示编码兼容的格式与SPIA。


（作者）----------Author(s)----------



Francesca Demichelis &lt;demichelis@science.unitn.it&gt;, Davide Prandi &lt;prandi@science.unitn.it&gt;


Maintainer: Davide Prandi &lt;prandi@science.unitn.it&gt;






参考文献----------References----------


Demichelis F, Greulich H, Macoska JA, Beroukhim R, Sellers WR, Garraway L, Rubin MA.  SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines.  Nucleic Acids Res. 2008;36:2446-2456.


实例----------Examples----------



library(SPIAssay)

# An example of genotype calls with:[一个例子基因型的调用方式：]
# - four cell lines[ - 四个单元系]
# - for each cell line five SNP calls[ - 每一个单元系5个SNP要求]
GenotypeCalls <- rbind(
c("SNP1", "AA", "AA", "AB", "AB"),
c("SNP2", "NoCall", "AA", "AB", "AB"),
c("SNP3", "AB", "AB", "AA" , "AB"),
c("SNP4", "BB", "BB", "BB", "BB"),
c("SNP5", "AB", "BB", "AA", "AA"))
colnames(GenotypeCalls) <- c("SNP_ID","CellLine1","CellLine2","CellLine3","CellLine4")

# Encode the data into SPIA format.[到SPIA的格式，对数据进行编码。]
# SPIA uses 0 for AA, 1 for BB, 2 for AB, and NA for NoCall[SPIA使用0为AA，BB，AB，NA NoCall]
# therefore, GenotypeCalls has to be encoded by meand of toSPIAData[因此，要被编码GenotypeCalls由劲歌的toSPIAData]
encoding <- c("AA","BB","AB","NoCall")
SPIAGenotypeCalls <- toSPIAData(GenotypeCalls,encoding)

# Perform SPIA analysis with parameters SPIAParam[执行的SPIA分析与参数SPIAParam]
SPIAParam <- list(Pmm = 0.1, nsigma = 1, Pmm_nonM = 0.6, nsigma_nonM = 1, PercValidCall=0.7)
SPIAanalysis <- SPIATest(SPIAGenotypeCalls, row.names = TRUE, test.prob = TRUE, SPIAParam)

# Plot SPIA pairwise comparison[图SPIA两两比较]
SPIAPlot(SPIAanalysis)

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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