anomSegStats(GWASTools)
anomSegStats()所属R语言包：GWASTools
Calculate LRR and BAF statistics for anomalous segments
计算异常段LRR和曝气生物滤池统计
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculate LRR and BAF statistics for anomalous segments and plot results
LRR和曝气生物滤池统计计算异常段和图结果
用法----------Usage----------
anomSegStats(intenData, genoData, snp.ids, anom, centromere,
lrr.cut = -2, verbose = TRUE)
anomStatsPlot(intenData, genoData, anom.stats, snp.ineligible,
plot.ineligible = FALSE, centromere = NULL,
brackets = c("none", "bases", "markers"), brkpt.pct = 10,
whole.chrom = FALSE, win = 5, win.calc = FALSE, win.fixed = 1,
zoom = c("both", "left", "right"), info = NULL, cex = 0.5)
参数----------Arguments----------
参数：intenData
An IntensityData object containing BAlleleFreq and LogRRatio. The order of the rows of intenData and the snp annotation are expected to be by chromosome and then by position within chromosome.
IntensityData对象含有BAlleleFreq和LogRRatio的。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。
参数：genoData
A GenotypeData object. The order of the rows of intenData and the snp annotation are expected to be by chromosome and then by position within chromosome.
一个GenotypeData对象。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。
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 IDS“的向量。一般排除失败和强度仅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：anom
data.frame of detected chromosome anomalies. Names must include "scanID", "chromosome", "left.index", "right.index", "sex", "method", "anom.id". Valid values for "method" are "BAF" or "LOH" referring to whether the anomaly was detected by BAF method (anomDetectBAF) or by LOH method (anomDetectLOH). Here "left.index" and "right.index" are row indices of intenData with left.index < right.index.
检测染色体异常的数据框。名称必须包括“scanID”，“染色体”，“left.index”，“right.index”，“性别”，“方法”，“anom.id”。 “办法”的有效值“燃油附加费”或“蕙”指曝气生物滤池法（anomDetectBAF）或蕙方法（anomDetectLOH）检测是否异常。在这里，“left.index”和“right.index”的intenData排指数与left.index <right.index的。
参数：centromere
data.frame with centromere position info. Names must include "chrom", "left.base", "right.base". Valid values for "chrom" are 1:22, "X", "Y", "XY". Here "left.base" and "right.base" are start and end base positions of the centromere location, respectively.
与着丝点位置信息的数据框。名称必须包括“铬”，“left.base”，“right.base”。有效的值是1:22，“铬”的“X”型，“Y”，“XY”。这里的“left.base”和“right.base”的开始和结束的着丝点位置的基本立场，分别。
参数：lrr.cut
count the number of eligible LRR values less than lrr.cut
计数资格LRR类值的数量比lrr.cut
参数：verbose
whether to print the scan id currently being processed
是否要打印扫描身份证目前正在处理中
参数：anom.stats
data.frame of chromosome anomalies with statstics, usually the output of anomSegStats. Names must include "anom.id", "scanID", "chromosome", "left.index", "right.index", "method", "nmark.all", "nmark.elig", "left.base", "right.base", "nbase", "non.anom.baf.med", "non.anom.lrr.med", "anom.baf.dev.med", "anom.baf.dev.5", "anom.lrr.med", "nmark.baf", "nmark.lrr". Left and right refer to start and end, respectively, of the anomaly, in position order.
染色体异常与statstics通常anomSegStats的输出的数据框。名称包括的“anom.id”，“scanID”，“染色体”，“left.index”，“right.index”，“方法”，“nmark.all”，“nmark。 elig“，”left.base“，”right.base“，”n基准“，”non.anom.baf.med“，”non.anom.lrr.med的“，”anom.baf。 dev.med“，”anom.baf.dev.5“，”anom.lrr.med“，”nmark.baf“，”nmark.lrr“。左，右指开始和结束，分别为异常的位置顺序，。
参数：snp.ineligible
vector of ineligible snp ids (e.g., intensity-only, failed snps, XTR and HLA regions). See HLA and pseudoautosomal.
向量，不合格的SNP ID（例如，仅强度，失败的SNPs，XTR的和HLA区域）。看到HLA和pseudoautosomal。
参数：plot.ineligible
whether or not to include ineligible points in the plot for LogRRatio
是否或不包括在图LogRRatio不合格
参数：brackets
type of brackets to plot around breakpoints - none, use base length, use number of markers (note that using markers give asymmetric brackets); could be used, along with brkpt.pct, to assess general accuracy of end points of the anomaly
括号内的类型，绘制周围断点 - 没有使用碱基的长度，使用标记（注意，使用标记给非对称的括号内）;可以使用，随着brkpt.pct，评估一般精度异常的终点
参数：brkpt.pct
percent of anomaly length in bases (or number of markers) for width of brackets
括号宽度％的异常碱基的长度（或标记的数量）
参数：whole.chrom
logical to plot the whole chromosome or not (overrides win and zoom)
逻辑绘制整条染色体或不（覆盖win和zoom）
参数：win
size of the window (a multiple of anomaly length) surrounding the anomaly to plot
周围的异常绘制窗口大小（异常长度的倍数）
参数：win.calc
logical to calculate window size from anomaly length; overrides win and gives window of fixed length given by win.fixed
逻辑来计算窗口的大小，从异常的长度;覆盖win和固定长度的窗口win.fixed
参数：win.fixed
number of megabases for window size when win.calc=TRUE
碱基数为窗口大小的时候win.calc=TRUE
参数：zoom
indicates whether plot includes the whole anomaly ("both") or zooms on just the left or right breakpoint; "both" is default
图指示是否包括整个异常（“既”），或只是左或右的断点放大“既”是默认
参数：info
character vector of extra information to include in the main title of the upper plot
字符的额外的信息向量，包括在主标题上的图
参数：cex
cex value for points on the plots
CEX价值为图上的点
Details
详情----------Details----------
anomSegStats computes various statistics of the input anomalies. Some of these are basic statistics for the characteristics of the anomaly and for measuring deviation of LRR or BAF from expected. Other statistics are used in downstrean quality control analysis, including detecting terminal anomalies and investigating centromere-spanning anomalies.
anomSegStats计算输入异常的各种统计数据。其中有些是基本统计异常的特点和LRR类或BAF从预计的测量偏差。其他统计在downstrean质量控制分析，包括终端异常检测和调查横跨着丝粒的异常。
anomStatsPlot produces separate png images of each anomaly stored in the working directory from which the program is called. Each image consists of an upper plot of LogRRatio values and a lower plot of BAlleleFrequency values for a zoomed region around the anomaly or whole chromosome (depending up parameter choices). Each plot has vertical lines demarcating the anomaly and horizontal lines displaying certain statistics from anomSegStats. The upper plot title includes sample number and chromosome. Further plot annotation describes which anomaly statistics are represented.
anomStatsPlot产生单独的png图像，从该方案被称为工作目录中存储的每个异常。每幅图像由上图LogRRatio值和缩小区域周围的异常或整条染色体（取决于参数选择）BAlleleFrequency值较低的图。每个小区都有划定的异常和某些统计数字显示，从anomSegStats水平线的垂直线。上图标题包括样本数和染色体。进一步的图注解说明哪些异常的统计资料表示。
值----------Value----------
anomSegStats produces a data.frame with the variables for anom plus the following columns: Left and right refer to position order with left < right.
anomSegStatsanom加上下面列的变量产生一个数据框：左和右是指定位<右左的顺序。
参数：nmark.all
total number of SNP markers on the array from left.index to right.index inclusive
SNP标记数组从left.index到right.index包容总数
参数：nmark.elig
total number of eligible SNP markers on the array from left.index to right.index, inclusive. See snp.ids for definition of eligible SNP markers.
总数阵列上的合资格的SNP标记从left.index以right.index，包容性。看到snp.ids合资格的SNP标记的定义。
参数：left.base
base position corresponding to left.index
碱基位置对应left.index
参数：right.base
base position corresponding to right.index
碱基位置对应right.index
参数：nbase
number of bases from left.index to right.index, inclusive
数量的碱基从left.index以right.index，包容
参数：non.anom.baf.med
BAF median of non-anomalous segments on all autosomes for the associated sample, using eligible heterozygous or missing SNP markers
曝气生物滤池非异常段使用资格的杂合子或失踪SNP标记对相关样本的所有染色体中位数，
参数：non.anom.lrr.med
LRR median of non-anomalous segments on all autosomes for the associated sample, using eligible SNP markers
LRR类非异常段使用资格的SNP标记对相关样本的所有染色体中位数，
参数：non.anom.lrr.mad
MAD for LRR of non-anomalous segments on all autosomes for the associated sample, using eligible SNP markers
气LRR类非反常段的相关样本的所有染色体上使用资格的SNP标记，
参数：anom.baf.dev.med
BAF median of deviations from non.anom.baf.med of points used to detect anomaly (eligible and heterozygous or missing)
曝气生物滤池中位数从偏离non.anom.baf.med点，用于检测异常（资格和杂合子或丢失）
参数：anom.baf.dev.5
median of BAF deviations from 0.5, using eligible heterozygous or missing SNP markers in anomaly
中位数从0.5曝气生物滤池的偏差，使用资格的杂合子或失踪的SNP标记异常
参数：anom.baf.dev.mean
mean of BAF deviations from non.anom.baf.med, using eligible heterozygous or missing SNP markers in anomaly
意味着来自non.anom.baf.med，使用资格的杂合子或失踪的SNP标记在异常的曝气生物滤池的偏差
参数：anom.baf.sd
standard deviation of BAF deviations from non.anom.baf.med, using eligible heterozygous or missing SNP markers in anomaly
non.anom.baf.med，使用资格的杂合子或失踪的SNP标记在异常曝气生物滤池偏差的标准偏差
参数：anom.baf.mad
MAD of BAF deviations from non.anom.baf.med, using eligible heterozygous or missing SNP markers in anomaly
曝气生物滤池偏差疯狂non.anom.baf.med，使用资格的杂合子或失踪的SNP标记在异常
参数：anom.lrr.med
LRR median of eligible SNP markers within the anomaly
LRR类中位数为合资格的SNP标记内的异常
参数：anom.lrr.sd
standard deviation of LRR for eligible SNP markers within the anomaly
LRR类为合资格的SNP标记在异常的标准偏差
参数：anom.lrr.mad
MAD of LRR for eligible SNP markers within the anomaly
MAD的LRR类为合资格的SNP标记内的异常
参数：nmark.baf
number of SNP markers within the anomaly eligible for BAF detection (eligible markers that are heterozygous or missing)
SNP标记内的异常曝气生物滤池的检测资格（资格的标志是杂合子或丢失）
参数：nmark.lrr
number of SNP markers within the anomaly eligible for LOH detection (eligible markers)
资格SNP标记内的异常为蕙检测（合资格的标志）
参数：cent.rel
position relative to centromere - left, right, span
着丝粒 - 左，右，大跨度的相对位置
参数：left.most
T/F for whether the anomaly is the left-most anomaly for this sample-chromosome, i.e. no other anomalies with smaller start base position
/ F是否异常是最左边的样品染色体异常，即与规模较小的基础地位没有其他异常
参数：right.most
T/F whether the anomaly is the right-most anomaly for this sample-chromosome, i.e. no other anomalies with larger end base position
T / F是否异常是最右边的样品染色体异常，即具有较大的一端碱基的地位没有其他异常
参数：left.last.elig
T/F for whether the anomaly contains the last eligible SNP marker going to the left (decreasing position)
异常是否包含最后的资格去左边（降低位置的SNP标记的T / F）
参数：right.last.elig
T/F for whether the anomaly contains the last eligible SNP marker going to the right (increasing position)
异常是否包含最后的合资格的SNP标记的权利（增加位置的T / F）
参数：left.term.lrr.med
median of LRR for all eligible SNP markers from left-most eligible marker to the left telomere (only calculated for the most distal anom)
LRR类的中位数为所有合资格的SNP标记从左侧最有资格的标志左边的端粒（只计算最远端的ANOM）
参数：right.term.lrr.med
median of LRR for all eligible markers from right-most eligible marker to the right telomere (only calculated for the most distal anom)
中位数为所有权利，最有资格的标志，以正确的端粒的资格标记的LRR类（只计算最远端的ANOM）
参数：left.term.lrr.n
sample size for calculating left.term.lrr.med
样本大小计算left.term.lrr.med
参数：right.term.lrr.n
sample size for calculating right.term.lrr.med
样本大小计算right.term.lrr.med
参数：cent.span.left.elig.n
number of eligible markers on the left side of centromere-spanning anomalies
数量上的着丝粒的跨越异常左侧资格标记
参数：cent.span.right.elig.n
number of eligible markers on the right side of centromere-spanning anomalies
合资格的标志上的着丝粒的跨越异常右侧
参数：cent.span.left.bases
length of anomaly (in bases) covered by eligible markers on the left side of the centromere
覆盖着丝粒的左侧资格标记异常的长度（碱基）
参数：cent.span.right.bases
length of anomaly (in bases) covered by eligible markers on the right side of the centromere
异常的长度（碱基）所涵盖的合资格的标志上的着丝粒的右侧
参数：cent.span.left.index
index of eligible marker left-adjacent to centromere; recall that index refers to row indices of intenData
合资格的标志左侧相邻的着丝粒指数;召回该指数是指排intenData指数
参数：cent.span.right.index
index of elig marker right-adjacent to centromere
elig标记指数右相邻着丝粒
参数：bafmetric.anom.mean
mean of BAF-metric values within anomaly, using eligible heterozygous or missing SNP markers BAF-metric values were used in the detection of anomalies. See anomDetectBAF for definition of BAF-metric
曝气生物滤池内异常度量值意味着，使用资格的杂合子或失踪SNP标记的曝气生物滤池度量值，用于检测异常。看到anomDetectBAF曝气生物滤池度量的定义
参数：bafmetric.non.anom.mean
mean of BAF-metric values within non-anomalous segments across all autosomes for the associated sample, using eligible heterozygous or missing SNP markers
曝气生物滤池十进制值意味着非异常段使用资格的杂合子或失踪SNP标记在相关样本的所有染色体内，
参数：bafmetric.non.anom.sd
standard deviation of BAF-metric values within non-anomalous segments across all autosomes for the associated sample, using eligible heterozygous or missing SNP markers
曝气生物滤池内非跨所有相关样品染色体异常段，使用资格的杂合子或失踪SNP标记，度量值的标准偏差
参数：nmark.lrr.low
number of eligible markers within anomaly with LRR values less than lrr.cut
LRR类值在合资格的标志异常数量比lrr.cut
注意----------Note----------
The non-anomalous statistics are computed over all autosomes for the sample associated with an anomaly. Therefore the accuracy of these statistics relies on the input anomaly data.frame including all autosomal anomalies for a given sample.
非异常的统计数据，计算了样品所有染色体异常关联。因此，这些统计数据的准确性依赖于输入异常数据框，包括一个给定的样本中的所有染色体异常。
作者（S）----------Author(s)----------
Cathy Laurie
参见----------See Also----------
anomDetectBAF, anomDetectLOH
anomDetectBAF，anomDetectLOH
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]
snp.failed <- snpAnnot$snpID[snpAnnot$missing.n1 == 1]
# example results from anomDetectBAF[从anomDetectBAF例子的结果]
baf.anoms <- data.frame("scanID"=scan.ids[1],"chromosome"=21,
"left.index"=100,"right.index"=200, sex="M", method="BAF",
anom.id=1)
# example results from anomDetectLOH[从anomDetectLOH例子的结果]
loh.anoms <- data.frame("scanID"=scan.ids[2],"chromosome"=22,
"left.index"=400,"right.index"=500, sex="F", method="LOH",
anom.id=2)
anoms <- rbind(baf.anoms, loh.anoms)
data(centromeres.hg18)
stats <- anomSegStats(blData, genoData, snp.ids=snp.ids, anom=anoms,
centromere=centromeres.hg18)
anomStatsPlot(blData, genoData, anom.stats=stats,
snp.ineligible=snp.failed, centromere=centromeres.hg18)
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 21:21:15
