anomDetectLOH(GWASTools)
anomDetectLOH()所属R语言包：GWASTools
LOH Method for Chromosome Anomaly Detection
蕙方法为染色体异常检测
译者：生物统计家园网 机器人LoveR
描述----------Description----------
anomDetectLOH breaks a chromosome up into segments of homozygous runs of SNP markers determined by change points in Log R Ratio and selects segments which are likely to be anomalous.
anomDetectLOH打破染色体成合子运行logR比率的变化点确定，并选择有可能是异常的段的SNP标记段。
用法----------Usage----------
anomDetectLOH(intenData, genoData, scan.ids, chrom.ids, snp.ids,
known.anoms, smooth = 50, min.width = 5, nperm = 10000, alpha = 0.001,
run.size = 50, inter.size = 4, homodel.min.num = 10, homodel.thresh = 10,
small.num = 20, small.thresh = 2.25, medium.num = 50, medium.thresh = 2,
long.num = 100, long.thresh = 1.5, small.na.thresh = 2.5,
length.factor = 5, merge.fac = 0.85, min.lrr.num = 20, verbose = TRUE)
参数----------Arguments----------
参数：intenData
An IntensityData object containing the Log R Ratio. The order of the rows of intenData and the snp annotation are expected to be by chromosome and then by position within chromosome. The scan annotation should contain sex, coded as "M" for male and "F" for female.
IntensityData对象包含logR比率。预计intenData和SNP注解行的顺序是由染色体，然后由内染色体上的位置。扫描注释应包含性别，代号为“M”代表男性和“F”为女性。
参数：genoData
A GenotypeData object. The order of the rows of genoData and the snp annotation are expected to be by chromosome and then by position within chromosome.
一个GenotypeData对象。预计行的genoData和SNP注解的顺序是由染色体，然后由内染色体上的位置。
参数：scan.ids
vector of scan ids (sample numbers) to process
IDS扫描矢量（样本数），以处理
参数：chrom.ids
vector of (unique) chromosomes to process
向量（唯一的）染色体处理
参数：snp.ids
vector of eligible snp ids. Usually exclude failed and intensity-only snps. Also recommended to exclude an HLA region on chromosome 6 and XTR region on chromosome 23 (X). See HLA and pseudoautosomal.
合资格的SNP ID向量。一般排除失败和强度的SNPs。还建议排除在6号染色体和23号染色体上的（X）的区域XTR的HLA区域。看到HLA和pseudoautosomal。
参数：known.anoms
data.frame of known anomalies (usually from anomDetectBAF); must have "scanID","chromosome","left.index","right.index". Here "left.index" and "right.index" are row indices of intenData. Left and right refer to start and end of anomaly, respectively, in position order.
已知的异常数据框（通常是从anomDetectBAF）;必须有“scanID”，“染色体”，“left.index”，“right.index”。这里“left.index”和“right.index”行intenData指数。左，右指开始和结束的异常，位置顺序，分别在。
参数：smooth
number of markers for smoothing region. See smooth.CNA in the DNAcopy package.
数平滑区域的标记。看到smooth.CNADNAcopy包。
参数：min.width
minimum number of markers for segmenting. See segment in the DNAcopy package.
分割标记的最低数量。看到segmentDNAcopy包。
参数：nperm
number of permutations. See segment in the DNAcopy package.
排列数。看到segmentDNAcopy包。
参数：alpha
significance level. See segment in the DNAcopy package.
显着水平。看到segmentDNAcopy包。
参数：run.size
number of markers to declare a 'homozygous' run (here 'homozygous' includes homozygous and missing)
标记的数量，申报一个“纯合子”运行（这里“纯合子”包括纯合缺失）
参数：inter.size
number of consecutive heterozygous markers allowed to interrupt a 'homozygous' run
允许中断一个“纯合子”运行连续的杂合标记的数量
参数：homodel.min.num
minimum number of markers to detect extreme difference in lrr (for homozygous deletion)
最低数量标志物检测在LRR极端的差异（缺失）
参数：homodel.thresh
threshold for measure of deviation from non-anomalous needed to declare segment a homozygous deletion.
阈值需要申报分割缺失非异常偏差的措施。
参数：small.num
minimum number of SNP markers to declare segment as an anomaly (other than homozygous deletion)
最低数量的SNP标记来声明段作为一个异常（缺失）
参数：small.thresh
threshold for measure of deviation from non-anomalous to declare segment anomalous if number of SNP markers is between small.num and medium.num.
非异常的偏差的措施，声明段异常SNP标记的数量是small.num和medium.num之间的阈值。
参数：medium.num
threshold for number of SNP markers to identify 'medium' size segment
SNP的数量阈值标记，以确定“中等”尺寸段
参数：medium.thresh
threshold for measure of deviation from non-anomalous needed to declare segment anomalous if number of SNP markers is between medium.num and long.num.
阈值的声明段异常SNP标记的数量是medium.num和long.num之间所需的非异常偏差的措施。
参数：long.num
threshold for number of SNP markers to identify 'long' size segment
SNP的数量阈值标记，以确定长尺寸段
参数：long.thresh
threshold for measure of deviation from non-anomalous when number of markers is bigger than long.num
从非异常偏差的措施的阈值时，标记的数量是更大的比long.num
参数：small.na.thresh
threshold measure of deviation from non-anomalous when number of markers is between small.num and medium.num and 'local mad.fac' is NA. See Details section for definition of 'local mad.fac'.
阈值的偏差从非反常的措施时，标记的数量之间small.num和medium.num和地方mad.fac“是NA。详细定义当地mad.fac“节。
参数：length.factor
window around anomaly defined as length.factor*(no. of markers in segment) on either side of the given segment. Used in determining 'local mad.fac'. See Details section.
周围定义为异常的窗口length.factor*（编号标记段）定段两侧。用于确定当地mad.fac“。见详图。
参数：merge.fac
threshold for 'sd.fac'= number of baseline standard deviations of segment mean from baseline mean; consecutive segments with 'sd.fac' above threshold are merged
阈值sd.fac=段基线标准偏差数，是指从基线的平均;sd.fac阈值以上的连续段合并
参数：min.lrr.num
if any 'non-anomalous' interval has fewer markers than min.lrr.num, interval is ignored in finding non-anomalous baseline unless it's the only piece left
如果任何“非异常的间隔有比min.lrr.num少的标记，发现异常非基线间隔中被忽略，除非它是剩下的唯一一块
参数：verbose
logical indicator whether to print the scan id currently being processed
目前正在处理的逻辑指示灯是否打印扫描ID
Details
详情----------Details----------
Detection of anomalies with loss of heterozygosity accompanied by change in Log R Ratio. Male samples for chromosome 23 (X) are not processed.
杂合性丢失logR比率的变化伴随着异常的检测。男23号染色体（X）的样本不被处理。
Circular binary segmentation (CBS) (using the R-package DNAcopy) is applied to LRR values and, in parallel, runs of homozygous or missing genotypes of a certain minimal size (run.size) (and allowing for some interruptions by no more than inter.size heterozygous SNPs ) are identified. Intervals from known.anoms are excluded from the identification of runs. After some possible merging of consecutive CBS segments (based on satisfying a threshold merge.fac for deviation from non-anomalous baseline), the homozygous runs are intersected with the segments from CBS.
循环二元分割（CBS）的（使用的R-包DNAcopy）应用LRR类值，平行，合子基因型或失踪的某一个最小尺寸（run.size）（，并允许运行一些干扰比inter.size杂合子的SNPs）被确定。从known.anoms间隔排除从奔跑鉴定。可能合并后，一些连续CBS段（基于满足阈值merge.fac非异常基线偏离），纯合的运行是从CBS段相交。
Determination of anomalous segments is based on a combination of number-of-marker thresholds and deviation from a non-anomalous baseline. Segments are declared anomalous if deviation from non-anomalous is above corresponding thresholds. (See small.num, small.thresh, medium.num,medium.thresh, long.num,long.thresh,and small.na.thresh.) Non-anomalous median and MAD are defined for each sample-chromosome combination. Intervals from known.anoms and the homozygous runs identified are excluded; remaining regions are the non-anomalous baseline.
基于标记数量阈值和非异常的基线偏离组合异常段的测定。段申报异常，如果从非异常偏差是相应的阈值以上。 （见small.num，small.thresh，medium.num，medium.thresh，long.num，long.thresh，small.na.thresh）。非异常位数和MAD定义为每个样品的染色体组合。从间隔known.anoms“纯合子运行确定被排除在外;其余区域的非异常的基线。
Deviation from non-anomalous is measured by a combination of a chromosome-wide 'mad.fac' and a 'local mad.fac' (both the average and the minimum of these two measures are used). Here 'mad.fac' is (segment median-non-anomalous median)/(non-anomalous MAD) and 'local mad.fac' is the same definition except the non-anomalous median and MAD are computed over a window including the segment (see length.factor). Median and MADare found for eligible LRR values.
从非异常偏差测量染色体全mad.fac和地方mad.fac“（平均和最低的这两项措施）的组合。这里mad.fac“（段中位数非异常的中位数）/（非异常MAD）的当地mad.fac”除非异常的中位数和MAD的一个窗口，包括段计算的定义相同（见length.factor）。为合资格的LRR类值中位数和MADare发现。
值----------Value----------
A list with the following elements:
具有下列内容的列表：
参数：raw
raw homozygous run data, not including any regions present in known.anoms. A data.frame with the following columns: Left and right refer to start and end of anomaly, respectively, in position order.
原料的纯合的运行数据，不包括任何区域，目前在known.anoms。一个数据框与下面的列：左和右是指开始和结束的异常，位置顺序，分别在。
left.index: row index of intenData indicating left endpoint of segment
left.index：intenData的行的索引说明段的左边端点
right.index: row index of intenData indicating right endpoint of segment
right.index：intenData的行的索引，指示段右端点
left.base: base position of left endpoint of segment
left.base：段左端点的基础地位
right.base: base position of right endpoint of segment
right.base：段右端点的基础地位
scanID: integer id of scan
scanID整数ID：扫描
chromosome: chromosome as integer with 23 representing X
23 chromosome：染色体为整数，代表X
参数：raw.adjusted
data.frame of runs after merging and intersecting with CBS segments, with the following columns: Left and right refer to start and end of anomaly, respectively, in position order.
合并，并与CBS段相交，与下面的列：左，右指开始和结束的异常，位置顺序，分别在后运行数据框。
scanID: integer id of scan
scanID整数ID：扫描
chromosome: chromosome as integer with 23 representing X
23 chromosome：染色体为整数，代表X
left.index: row index of intenData indicating left endpoint of segment
left.index：intenData的行的索引说明段的左边端点
right.index: row index of intenData indicating right endpoint of segment
right.index：intenData的行的索引，指示段右端点
left.base: base position of left endpoint of segment
left.base：段左端点的基础地位
right.base: base position of right endpoint of segment
right.base：段右端点的基础地位
num.mark: number of eligible SNP markers in segment
num.mark：符合条件的SNP标记段
seg.median: median of eligible LRR values in segment
seg.median：段资格LRR类值中位数
seg.mean: mean of eligible LRR values in segment
seg.mean“：指段资格LRR类值
mad.fac: measure of deviation from non-anomalous baseline, equal to abs(median of segment - baseline median)/(baseline MAD); used in determining anomalous segments
mad.fac：在确定使用的异常段措施偏离非异常基准，等于ABS（中位数段 - 基线中位数）/（基线疯狂）;
sd.fac: measure of deviation from non-anomalous baseline, equal to abs(mean of segment - baseline mean)/(baseline standard deviation); used in determining whether to merge
sd.fac：测量偏差非异常基准，等于ABS（指段 - 基线平均）/（基线标准偏差）;在决定是否合并使用
local: measure of deviation from non-anomalous baseline used equal to abs(median of segment - local baseline median)/(local baseline MAD); local baseline consists of eligible LRR values in a window around segment; used in determining anomalous segments
local：用于测量从非异常基线的偏差等于ABS（中位数段 - 当地基线中位数）/（当地基线疯狂）;当地的基准资格LRR类值在各地段的窗口组成;用于确定反常段
num.segs: number of segments found by CBS for the given chromosome
num.segs：为给定的染色体由CBS的段数
chrom.nonanom.mad: MAD of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.mad：资格LRR类值在整个染色体异常区域疯狂
chrom.nonanom.median: median of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.median：在整个染色体非异常区的资格LRR类值中位数
chrom.nonanom.mean: mean of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.mean“：指在整个染色体非异常区的资格LRR类值
chrom.nonanom.sd: standard deviation of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.sd：在整个染色体非异常区的资格LRR类值的标准偏差
sex: sex of the scan id coded as "M" or "F"
sex：性别扫描ID编码为“M”或“F”
参数：filtered
data.frame of the segments identified as anomalies. Columns are the same as in raw.adjusted.
数据框确定为异常的段。列是作为raw.adjusted相同。
参数：base.info
data.frame with columns:
数据框的列：
chrom.nonanom.mad: MAD of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.mad：资格LRR类值在整个染色体异常区域疯狂
chrom.nonanom.median: median of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.median：在整个染色体非异常区的资格LRR类值中位数
chrom.nonanom.mean: mean of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.mean“：指在整个染色体非异常区的资格LRR类值
chrom.nonanom.sd: standard deviation of eligible LRR values in non-anomalous regions across the chromosome
chrom.nonanom.sd：在整个染色体非异常区的资格LRR类值的标准偏差
sex: sex of the scan id coded as "M" or "F"
sex：性别扫描ID编码为“M”或“F”
num.runs: number of original homozygous runs found for given scan/chromosome
num.runs：原合子运行的数量给定的扫描/染色体
num.segs: number of segments for given scan/chromosome produced by CBS
num.segs：给定段人数由CBS制作的扫描/染色体
scanID: integer id of scan
scanID整数ID：扫描
chromosome: chromosome as integer, with 23 representing X
chromosome：23个代表X染色体为整数，
sex: sex of the scan id coded as "M" or "F"
sex：性别扫描ID编码为“M”或“F”
参数：segments
data.frame of the segmentation found by CBS with columns:
数据框的发现与列由CBS分割：
scanID: integer id of scan
scanID整数ID：扫描
chromosome: chromosome as integer, with 23 representing X
chromosome：23个代表X染色体为整数，
left.index: row index of intenData indicating left endpoint of segment
left.index：intenData的行的索引说明段的左边端点
right.index: row index of intenData indicating right endpoint of segment
right.index：intenData的行的索引，指示段右端点
left.base: base position of left endpoint of segment
left.base：段左端点的基础地位
right.base: base position of right endpoint of segment
right.base：段右端点的基础地位
num.mark: number of eligible SNP markers in the segment
num.mark：合资格的SNP标记在数段
seg.mean: mean of eligible LRR values in the segment
seg.mean“：指段的资格LRR类值
sd.fac: measure of deviation from baseline equal to abs(mean of segment - baseline mean)/(baseline standard deviation) where the baseline is over non-anomalous regions
sd.fac：从基线的偏差等于ABS（指段 - 基线平均）/（基线标准偏差）基线非异常区的措施
参数：merge
data.frame of scan id/chromosome pairs for which merging occurred.
而兼并发生的扫描ID /对染色体的数据框。
scanID: integer id of scan
scanID整数ID：扫描
chromosome: chromosome as integer, with 23 representing X
chromosome：23个代表X染色体为整数，
作者（S）----------Author(s)----------
Cecelia Laurie
参考文献----------References----------
参见----------See Also----------
segment and smooth.CNA in the package DNAcopy, also findBAFvariance, anomDetectLOH
segment和smooth.CNA包DNAcopy，findBAFvariance，anomDetectLOH的
举例----------Examples----------
library(GWASdata)
data(illumina_scan_annot)
scanAnnot <- ScanAnnotationDataFrame(illumina_scan_annot)
data(illumina_snp_annot)
snpAnnot <- SnpAnnotationDataFrame(illumina_snp_annot)
blfile <- system.file("extdata", "illumina_bl.nc", package="GWASdata")
blnc <- NcdfIntensityReader(blfile)
blData <- IntensityData(blnc, scanAnnot=scanAnnot, snpAnnot=snpAnnot)
genofile <- system.file("extdata", "illumina_geno.nc", package="GWASdata")
genonc <- NcdfGenotypeReader(genofile)
genoData <- GenotypeData(genonc, scanAnnot=scanAnnot, snpAnnot=snpAnnot)
scan.ids <- scanAnnot$scanID[1:2]
chrom.ids <- unique(snpAnnot$chromosome)
snp.ids <- snpAnnot$snpID[snpAnnot$missing.n1 < 1]
# example for known.anoms, would get this from anomDetectBAF[例如为known.anoms，会得到从anomDetectBAF这]
known.anoms <- data.frame("scanID"=scan.ids[1],"chromosome"=21,
"left.index"=100,"right.index"=200)
LOH.anom <- anomDetectLOH(blData, genoData, scan.ids=scan.ids,
chrom.ids=chrom.ids, snp.ids=snp.ids, known.anoms=known.anoms)
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 21:20:57
