locateVariants(VariantAnnotation)
locateVariants()所属R语言包：VariantAnnotation
Locate variants
找到变种
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Identify variant location with respect to gene functionality
确定变异基因的功能方面的位置
用法----------Usage----------
locateVariants(query, subject, ...)
## S4 method for signature 'GRanges,TranscriptDb'
locateVariants(query, subject, ...)
参数----------Arguments----------
参数：query
A GRanges object containing the variants
一个农庄的对象，其中包含的变种
参数：subject
A TranscriptDb object that will serve as the annotation reference
一个TranscriptDb对象，将作为注释的参考
参数：...
Additional arguments passed to methods
额外的参数传递给方法
Details
详情----------Details----------
Range representation :
范围表示：
locateVariants accepts a GRanges object that contains the variants of interest. The range should reflect the positions of the reference basepairs being substituted or deleted. The width will be the same as the number of basepairs being substituted or deleted. For insertions, the width is negative and the range is represented as start = end + 1. For examples of how different variant types should be represented see the variants sample data in the package.
locateVariants接受农庄对象，包含利益的变种。范围应反映的参考碱基对的位置被取代或删除。宽度将被替换或删除的碱基对数目相同。对于插入，宽度是负和start=end1表示的范围。对于如何应代表不同的变异类型，见variants包中的样本数据的例子。
Location :
地点：
Variant positions are overlaped with feature ranges of the TranscriptDb object. Possible locations include coding, intron, 3UTR, 5UTR, intergenic or unknown. Intergenic variants are those that do not match (i.e., overlap with) a transcript. Currently all findOverlaps operations in locateVariants are performed with type = "within". This requires that the variant fall completely within one of the defined regions or else it is classified as "unknown".
变种位置overlaped功能的TranscriptDb对象范围。可能的地点包括编码，内含子，3UTR，5UTR，间隔或未知。间隔的变种，是那些不匹配（即重叠）成绩单。目前所有findOverlaps的操作locateVariants与type=执行“内”。这需要的变种完全属于内定义的区域之一，否则它被归类为“未知”。
值----------Value----------
A DataFrame is returned with columns of queryHits, txID, geneID and Location. queryHits is a map back to the original variants from the query. The txID and geneID values come from the TranscriptDb object. For intergenic variants, the geneID contains identifiers for genes on either side of the variant (preceding and following). Each row in the result represents a transcript hit by a variant. When a variant hits multiple transcripts there will be multiple rows for that variant.
一个DataFrame返回列queryHits，txID，geneID和Location。 queryHits回到query原变种图。 txID和geneID值从TranscriptDb对象的来。为间隔的变种，geneID包含任一侧的变异基因（之前和之后）的标识符。结果在每一行代表一个变种击中成绩单。当一个变种击中多个转录会有多行的变种。
作者（S）----------Author(s)----------
Valerie Obenchain
参见----------See Also----------
predictCoding
predictCoding
举例----------Examples----------
library(TxDb.Hsapiens.UCSC.hg18.knownGene)
library(BSgenome.Hsapiens.UCSC.hg18)
data(variants)
txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene
loc <- locateVariants(variants, txdb)
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 2012-2-26 15:56:48
