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R语言 beadarraySNP包 heterozygousSNPs()函数中文帮助文档(中英文对照)

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发表于 2012-2-25 12:35:41 | 显示全部楼层 |阅读模式
heterozygousSNPs(beadarraySNP)
heterozygousSNPs()所属R语言包:beadarraySNP

                                        Retrieve heterozygous SNPs
                                         检索杂合子的SNPs

                                         译者:生物统计家园网 机器人LoveR

描述----------Description----------

Heterozygous SNPs are determined based on quality score criteria
杂合子的SNPs质量评分标准的基础上确定


用法----------Usage----------


  heterozygousSNPs(object, threshold=0.9, useQuality=TRUE, relative=TRUE,



参数----------Arguments----------

参数:object
class SnpSetIllumina
类SnpSetIllumina


参数:threshold
numeric (0:1) minimum quality score to be called heterozygous
数字(0:1)的最低质量得分,被称为杂合子


参数:useQuality
logical, use quality score
逻辑,使用的质量得分


参数:relative
logical, use quality score relative to GTS, see details
逻辑,使用GTS的相对质量得分,查看详细信息


参数:percentile
logical, use percentage of probes above threshold
逻辑,使用比例高于阈值的探针


Details

详情----------Details----------

This function presumes that the specificity for determining heterozygity is  more important than the sensitivity, and will therefore only call probes heterozygous  if that can be done with high certainty.<br> The Illumina genotyping software calculates two quality measures: gen train score (GTS)  and gen call score (GCS). The GTS is a measure for how well clusters can be recognized  in a training set. This value is probe specific, and the same for all samples in an experiment. The GCS is a probe-specific, sample specific value that measures how close  a probe in a sample is to the clusters determined in the training step. This value is  always lower than the GTS for a probe.<br> read.SnpSetIllumina will put GCS into the callProbability element  of the assaydata slot and the GTS into the featureData slot. The  function uses these locations to retrieve the necessary information.<br> If relative is FALSE then the raw GCS values are compared to the threshold. In this case a threshold of around 0.5 should be used. If  relative is TRUE then GCS/GTS is compared to the threshold and threshold should be around 0.9.<br> With percentile=TRUE the threshold quantile is calculated for each sample, and only probes with higher scores can be called heterozygous. A threshold of around 0.2 seems to work fine usually.
这个函数假定特异性,确定heterozygity的是较重要的灵敏度,因此将只调用探针杂合子,如果可以做高确定性参考Illumina公司的基因分型软件计算两个质量的措施:(GTS的。根火车得分)和Gen呼叫评分(GCS)。 GTS的措施是如何聚类可以确认在训练集。这个值是具体的探针,所有样品相同,在一个实验。 GCS是特定探针,样品的特定值,测量样品探针是在训练步骤确定的聚类如何密切。此值始终比探针GTS较低。参考read.SnpSetIllumina将投入callProbability槽和GTS的元素,assaydata熙成featureData插槽。函数使用这些位置,以获取必要的信息。<br>如果relative是FALSE的原料GCS评分值相比threshold。在这种情况下,一个约0.5 threshold的应该被使用。如果relative是TRUE然后熙/ GTS是threshold和thresholdpercentile=TRUE threshold应该是约0.9。参考位数计算每个样品,只有分数较高的探针可以被称为杂合子。一个约0.2threshold似乎通常做工精细。


值----------Value----------

This function returns a logical matrix with same dimensions as object.
这个函数返回一个相同的尺寸为logical matrixobject。


注意----------Note----------

The purpose of the function is to separate heterozygous probes from non-heterozygous probes. In tumor samples the determination of the genotype can be difficult,  because of aneuploidy and the fact that a sample is often a mixture of normal and tumor cells.
该函数的目的是分开的非杂合探针杂合探针。在肿瘤样本基因型的决心是很困难的,因为非整倍体和样品往往是一个正常和肿瘤单元的混合物。


作者(S)----------Author(s)----------


Jan Oosting



参见----------See Also----------

SnpSetIllumina-class
SnpSetIllumina-class


举例----------Examples----------


  data(chr17.260)
  plot(heterozygosity(heterozygousSNPs(chr17.260[,"514TV"])),col="red",pch="x")
  points(heterozygosity(exprs(chr17.260)[,"514TV"]))

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。
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