BAFfromClusterMeans(GWASTools)
BAFfromClusterMeans()所属R语言包：GWASTools
B Allele Frequency & Log R Ratio Calculation
B等位基因频率和logR比率计算
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function calculates the B allele frequency and the log R ratio values from the mean R and theta values for each cluster. The values are written to a netCDF file which is assumed to exist with proper variables and size.
此函数计算的B等位基因频率和logR由比值为每个聚类的平均R和THETA值。值被写入到netCDF文件，这是假设存在适当的变量和大小。
用法----------Usage----------
BAFfromClusterMeans(intenData, bl.ncdf.filename,
clusterMeanVars = c("tAA","tAB","tBB","rAA","rAB","rBB"),
verbose = TRUE)
参数----------Arguments----------
参数：intenData
IntensityData object holding the X and Y intensity data from which the B allele frequency and log R ratio are calculated.
IntensityData对象举行的X和Y强度B等位基因频率和logR比计算数据。
参数：bl.ncdf.filename
The filepath for a previously created netCDF file to hold the B allele frequency and log R ratio values.
持有B等位基因频率为以前创建的netCDF文件的文件路径和登录R比率值。
参数：clusterMeanVars
Character vector indicating the names of the cluster mean columns in the SNP annotation of intenData. Must be in order (tAA,tAB,tBB,rAA,rAB,rBB).
特征向量表示聚类的名称，意思是单核苷酸多态性中的intenData的注释列。必须按顺序（TAA，TAB，TBB，RAA，RAB，RBB）。
参数：verbose
Logical value specifying whether to show progress information.
逻辑值，指定是否显示进度信息。
Details
详情----------Details----------
Because this function can take a considerable amount of time and space, sufficient attention should be given to the value used for block.size. The file specified by bl.ncdf.filename is assumed to have variables 'BAlleleFreq' and 'LogRRatio' to which the proper values are written.
由于此功能可以利用大量的时间和空间，应给予足够的重视价值block.size。 bl.ncdf.filename指定的文件假设有变量的BAlleleFreq和LogRRatio“被写入正确的价值观。
值----------Value----------
The netCDF file stored in the bl.ncdf.filename path is populated with values of B allele frequency and the log R ratio at the completion of this function.
netCDF文件存储在bl.ncdf.filename路径填充值B等位基因频率和R在完成这个功能比log。
作者（S）----------Author(s)----------
Stephanie Gogarten, Caitlin McHugh
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
# create IntensityData object from netCDF[从NetCDF的创建IntensityData对象]
library(GWASdata)
xyfile <- system.file("extdata", "illumina_qxy.nc", package="GWASdata")
xyNC <- NcdfIntensityReader(xyfile)
data(illumina_snp_annot)
snpAnnot <- SnpAnnotationDataFrame(illumina_snp_annot)
xyData <- IntensityData(xyNC, snpAnnot=snpAnnot)
nsamp <- nscan(xyData)
# create netCDF file to hold BAF/LRR data[创建netCDF文件保存曝气生物滤池/ LRR类数据]
blfile <- tempfile()
ncdfCreate(illumina_snp_annot, blfile, variables=c("BAlleleFreq","LogRRatio"), n.samples=nsamp)
# calculate BAF and LRR[计算曝气生物滤池和LRR]
BAFfromClusterMeans(xyData, blfile, verbose=FALSE)
# read output[读取输出]
blNC <- NcdfIntensityReader(blfile)
blData <- IntensityData(blNC)
baf <- getBAlleleFreq(blData)
lrr <- getLogRRatio(blData)
close(xyNC)
close(blNC)
file.remove(blfile)
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 21:21:56
