BAFfromGenotypes(GWASTools)
BAFfromGenotypes()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 for samples by either plate or by study. The values are written to a netCDF file which is assumed to exist with proper variables and size.
此函数计算无论是板或B等位基因频率和log比值R为样本，研究。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----------
BAFfromGenotypes(intenData, genoData,
bl.ncdf.filename, min.n.genotypes = 2,
call.method = c("by.plate", "by.study"),
plate.name = "plate",
block.size = 5000, 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：genoData
GenotypeData object.
GenotypeData对象。
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：min.n.genotypes
The minimum number of samples for each genotype at any SNP in order to have non-missing B allele freqency and log R ratio. Setting this parameter to 2 or a similar value is recommended.
以非丢失的等位基因B工频突变和logR比在任何SNP基因型为每个样本的最小数量。建议设置此参数为2或类似的价值。
参数：call.method
If call.method is 'by.plate', the B allele frequency and log R ratio are calculated for samples delineated by plates. This is the default method. If call.method is 'by.study', the calculation uses all samples at once. If a study does not have plate specifications, 'by.study' is the call.method that must be used.
，如果call.method是“by.plate，B等位基因频率和logR值计算板划定的样本。这是默认的方法。如果call.method是by.study“，计算使用的所有样本一次。如果研究没有板规格，by.study“是必须使用call.method。
参数：plate.name
Character string specifying the name of the plate variable in intenData or genoData. By default, the plate.name is simply 'plate' but oftentimes there are variations, such as 'plateID' or 'plate.num'.
字符串指定板的在intenData或genoData变量的名称。默认情况下，plate.name简直是“板”，但常常有变化，如plateID或plate.num“。
参数：block.size
An integer specifying the number of SNPs to be loaded from the netCDF file at one time. The recommended value is around 1000, but should vary depending on computing power.
从netCDF文件的SNPs数量的一个整数，指定要加载一次。建议值是1000左右，但应有所不同，具体取决于计算能力。
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)----------
Caitlin McHugh
参考文献----------References----------
<h3>See Also</h3> <code>IntensityData</code>, <code>GenotypeData</code>,
举例----------Examples----------
## Not run: [＃无法运行：]
# create IntensityData and GenotypeData objects from netCDF[从NetCDF的创建IntensityData和GenotypeData对象]
library(GWASdata)
data(affy_scan_annot)
scanAnnot <- ScanAnnotationDataFrame(affy_scan_annot)
nsamp <- nrow(scanAnnot)
data(affy_snp_annot)
snpAnnot <- SnpAnnotationDataFrame(affy_snp_annot)
xyfile <- system.file("extdata", "affy_qxy.nc", package="GWASdata")
xyNC <- NcdfIntensityReader(xyfile)
xyData <- IntensityData(xyNC, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
genofile <- system.file("extdata", "affy_geno.nc", package="GWASdata")
genoNC <- NcdfGenotypeReader(genofile)
genoData <- GenotypeData(genoNC, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
# 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(affy_snp_annot, blfile, variables=c("BAlleleFreq","LogRRatio"), n.samples=nsamp)
# calculate BAF and LRR[计算曝气生物滤池和LRR]
BAFfromGenotypes(xyData, genoData, blfile, min.n.genotypes=2,
call.method="by.plate", plate.name="plate")
blNC <- NcdfIntensityReader(blfile)
baf <- getBAlleleFreq(blNC)
lrr <- getLogRRatio(blNC)
close(xyData)
close(genoData)
close(blNC)
file.remove(blfile)
## End(Not run)[＃结束（不运行）]
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 2012-2-25 21:22:06
