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。
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发表于 2012-2-25 12:35:41
