findBAFvariance(GWASTools)
findBAFvariance()所属R语言包：GWASTools
Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation
查找与的高BAlleleFreq（或LogRRatio）标准差的染色体区域
译者：生物统计家园网 机器人LoveR
描述----------Description----------
sdByScanChromWindow uses a sliding window algorithm to calculate the standard deviation of the BAlleleFreq (or LogRRatio) values for a user specified number of bins across each chromosome of each scan.
sdByScanChromWindow使用一个滑动窗口算法来计算用户指定在每个染色体每次扫描的箱数的BAlleleFreq（或LogRRatio）值的标准偏差。
medianSdOverAutosomes calculates the median of the BAlleleFreq (or LogRRatio) standard deviation over all autosomes for each scan.
medianSdOverAutosomes计算的BAlleleFreq（或LogRRatio）对每次扫描所有染色体的标准偏差的中位数。
meanSdByChromWindow calculates the mean and standard deviation of the BAlleleFreq standard deviation in each window in each chromosome over all scans.
meanSdByChromWindow计算在每个染色体的所有扫描的BAlleleFreq在每个窗口的标准偏差的平均值和标准偏差。
findBAFvariance flags chromosomal areas with high BAlleleFreq standard deviation using previously calculated means and standard deviations over scans, typically results from sdByScanChromWindow.
findBAFvariance标记染色体区域高BAlleleFreq标准偏差使用先前计算的方法和标准偏差的扫描，通常从sdByScanChromWindow结果。
用法----------Usage----------
sdByScanChromWindow(intenData, genoData=NULL, var="BAlleleFreq", nbins=NULL,
snp.exclude=NULL, return.mean=FALSE, incl.miss=TRUE, incl.het=TRUE, incl.hom=FALSE)
medianSdOverAutosomes(sd.by.scan.chrom.window)
meanSdByChromWindow(sd.by.scan.chrom.window, sex)
findBAFvariance(sd.by.chrom.window, sd.by.scan.chrom.window,
sex, sd.threshold)
参数----------Arguments----------
参数：intenData
A IntensityData object
一个IntensityData对象
参数：genoData
A GenotypeData object. May be omitted if incl.miss, incl.het, and incl.hom are all TRUE, as there is no need to distinguish between genotype calls in that case.
一个GenotypeData对象。如果可以省略incl.miss，incl.het，incl.hom都TRUE，有没有必要区分基因型在这种情况下调用。
参数：var
The variable for which to calculate standard deviations, typically "BAlleleFreq" (the default) or "LogRRatio."
变量的计算标准偏差，典型的“BAlleleFreq”（默认）或“LogRRatio。”
参数：nbins
A vector with integers corresponding to the number of bins for each chromosome. The values all must be even integers.
与相应的每个染色体的垃圾桶数量的整数向量。所有的值必须是偶数。
参数：snp.exclude
An integer vector containing the snpIDs of SNPs to be excluded.
整数向量的SNP snpIDs被排除在外。
参数：return.mean
a logical. If TRUE, return mean as well as standard deviation.
一个逻辑。如果TRUE，返回的意思，以及标准偏差。
参数：incl.miss
a logical. If TRUE, include SNPs with missing genotype calls.
一个逻辑。如果TRUE，包括单核苷酸多态性与缺失基因型分型。
参数：incl.het
a logical. If TRUE, include SNPs called as heterozygotes.
一个逻辑。如果TRUE，包括单核苷酸多态性称为杂合子。
参数：incl.hom
a logical. If TRUE, include SNPs called as homozygotes. This is typically FALSE (the default) for BAlleleFreq calculations.
一个逻辑。如果TRUE，包括单核苷酸多态性称为纯合子。这通常是FALSE（默认）为BAlleleFreq计算。
参数：sd.by.scan.chrom.window
A list of matrices of standard deviation for each chromosome, with dimensions of number of scans x number of windows. This is typically the output of sdByScanChromWindow.
列表中的每个染色体的标准偏差矩阵，尺寸扫描X号窗口的数量。这通常是输出sdByScanChromWindow。
参数：sd.by.chrom.window
A list of matrices of the standard deviations, as generated by meanSdByChromWindow.
一个标准偏差的矩阵列表，生成meanSdByChromWindow。
参数：sex
A character vector of sex ("M"/"F") for the scans.
对性的特征向量（的“M”/“F”类）的扫描。
参数：sd.threshold
A value specifying the threshold for the number of standard deviations above the mean at which to flag.
一个值指定为上述标记的平均标准偏差数的阈值。
Details
详情----------Details----------
sdByScanChromWindow calculates the standard deviation of BAlleleFreq (or LogRRatio) values across chromosomes 1-22 and chromosome X for a specified number of 'bins' in each chromosome as passed to the function in the 'nbins' argument. The standard deviation is calculated using windows of width equal to 2 bins, and moves along the chromosome by an offset of 1 bin (or half a window). Thus, there will be a total of nbins-1 windows per chromosome. If nbins=NULL (the default), there will be 2 bins (one window) for each chromosome.
sdByScanChromWindow计算的BAlleleFreq（或LogRRatio）指定数量的“垃圾箱”，在每个染色体的1-22跨染色体和X染色体传递给函数在“nbins”参数值的标准偏差。使用窗口宽度等于2桶，沿染色体的移动计算的标准偏差1斌（或一个窗口的一半）的偏移。因此，将是一个总nbins-1每个染色体的Windows。如果nbins=NULL（默认），将每个染色体（一个窗口）2箱。
medianSdOverAutosomes calulates the median over autosomes of BAlleleFreq (or LogRRatio) standard deviations calculated for sliding windows within each chromosome of each scan. The standard deviations should be a list with one element for each chromosome, and each element consisting of a matrix with scans as rows.
medianSdOverAutosomescalulates过染色体BAlleleFreq（或LogRRatio）计算滑动窗口内每个染色体的每个扫描的标准差的中位数。标准偏差应该是每个染色体的一个元素的列表，每个元素作为行扫描矩阵组成。
meanSdByChromWindow calculates the mean and standard deviation over scans of BAlleleFreq standard deviations calculated for sliding windows within each chromosome of each scan. The BAlleleFreq standard deviations should be a list with one element for each chromosome, and each element consisting of a matrix containing the BAlleleFreq standard deviation for the i'th scan in the j'th bin. This is typically created using the sdByScanChromWindow function. For the X chromosome the calculations are separated out by gender.
meanSdByChromWindowBAlleleFreq标准偏差计算滑动窗口内每个染色体每次扫描的扫描，计算平均值和标准偏差。的BAlleleFreq标准偏差应该是每个染色体的一个元素的列表，每个元素包含的BAlleleFreq标准偏差为第i在第j个槽扫描矩阵组成。这通常是使用sdByScanChromWindow函数创建。的X染色体上分离出来，按性别计算。
findBAFvariance determines which chromosomes of which scans have regions which are at least a given number of SDs from the mean, using BAlleleFreq means and standard deviations calculated from sliding windows over each chromosome by scan.
findBAFvariance确定染色体扫描，其中有至少SDS平均的区域，使用BAlleleFreq手段和标准偏差计算滑动每个染色体由扫描窗口。
值----------Value----------
sdByScanChromWindow returns a list of matrices containing standard deviations. There is a matrix for each chromosome, with each matrix having dimensions of number of scans x number of windows. If return.mean=TRUE, two lists to matrices are returned, one with standard deviations and one with means.
sdByScanChromWindow返回一个包含标准偏差矩阵列表。有一个为每个染色体的矩阵，每个矩阵尺寸扫描X号窗口的数量。如果return.mean=TRUE，两个列表返回矩阵，一个标准偏差和手段之一。
medianSdOverAutosomes returns a data frame with colums "scanID" and "med.sd" containing the median standard deviations over all autosomes for each scan.
medianSdOverAutosomes返回colums“scanID”和“med.sd”包含了每次扫描所有染色体中位数标准偏差的数据框。
meanSdByChromWindow returns a list of matrices, one for each chromosome. Each matrix contains two columns called "Mean" and "SD", containing the mean and SD of the BAlleleFreq standard devations over scans for each bin. For the X chromosome the matrix has four columns "Female Mean", "Male Mean", "Female SD" and "Male SD".
meanSdByChromWindow返回一个矩阵列表，每个染色体之一。每个矩阵包含两列被称为“中庸”和“标清”，包含均值和BAlleleFreq标准devations通过扫描每个垃圾桶SD。矩阵的X染色体上有四列“女中庸”，“男中庸”，“SD雌性”和“雄性SD”。
findBAFvariance returns a matrix with columns "scanID", "chromosome", "bin", and "sex" containing those scan by chromosome combinations with BAlleleFreq standard deviations greater than those specified by sd.threshold.
findBAFvariance返回列“scanID”，“染色体”，“bin”的矩阵，和“性”含染色体组合BAlleleFreq比sd.threshold指定的标准偏差的扫描 。
作者（S）----------Author(s)----------
Caitlin McHugh, Cathy Laurie
参见----------See Also----------
IntensityData, GenotypeData, BAFfromClusterMeans, BAFfromGenotypes
IntensityData，GenotypeData，BAFfromClusterMeans，BAFfromGenotypes
举例----------Examples----------
library(GWASdata)
data(illumina_scan_annot)
scanAnnot <- ScanAnnotationDataFrame(illumina_scan_annot)
blfile <- system.file("extdata", "illumina_bl.nc", package="GWASdata")
blnc <- NcdfIntensityReader(blfile)
blData <- IntensityData(blnc, scanAnnot=scanAnnot)
genofile <- system.file("extdata", "illumina_geno.nc", package="GWASdata")
genonc <- NcdfGenotypeReader(genofile)
genoData <- GenotypeData(genonc, scanAnnot=scanAnnot)
nbins <- rep(8, 3) # need bins for chromosomes 21,22,23[需要染色体箱21,22,23的]
baf.sd <- sdByScanChromWindow(blData, genoData, nbins=nbins)
close(blData)
close(genoData)
med.res <- medianSdOverAutosomes(baf.sd)
sex <- scanAnnot$sex
sd.res <- meanSdByChromWindow(baf.sd, sex)
var.res <- findBAFvariance(sd.res, baf.sd, sex, sd.threshold=2)
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 21:23:19
