annotateVariants(R453Plus1Toolbox)
annotateVariants()所属R语言包：R453Plus1Toolbox
Adds genomic information to variants
添加到变异的基因组信息
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This method annotates given genomic variants (mutations). Annotation includes affected genes, exons and codons. Resulting amino acid changes are returned as well as dbSNP identifiers, if the mutation is already known. All information is fetched from Ensembl via biomaRt using the datasets
此方法诠释基因变异（突变）。注释包括受影响的基因，外显子和密码子。导致氨基酸的变化是返回以及dbSNP的标识符，如果已知的突变。所有的信息被提取通过biomaRt使用的数据集，从Ensembl的
用法----------Usage----------
annotateVariants(object, bsGenome)
参数----------Arguments----------
参数：object
A data frame storing variants or an instance of AVASet/MapperSet or a data frame (see details).
一个数据框存储变异或AVASet / MapperSet或一个数据框的实例（见详情）。
参数：bsGenome
An object of class BSGenome giving the genome to be used as reference sequence to calculate amino acid changes. This argument is only applicable when object is of type MapperSet. Default is "BSgenome.Hsapiens.UCSC.hg19". Note that the genome should fit to the Ensembl annotation.
一个类的对象BSGenome作为参考序列用于计算氨基酸的变化的基因组。这种说法是只适用于当object型MapperSet。默认是BSgenome.Hsapiens.UCSC.hg19“。需要注意的是基因组应符合Ensembl的注解。
Details
详情----------Details----------
If a data frame is given, the following columns must be present:
如果给出一个数据框，下面的列必须存在：
The rownames of the data frame are used as mutations' names (IDs). See examples for a properly defined data drame.
被用作基因突变的名字（IDS）数据框rownames的。见一个正确定义数据drame的的例子。
值----------Value----------
An object of class AnnotatedVariants. Affected genes, transcripts and exon as well as known SNPs are stored in a list-like structure. See the
对象类AnnotatedVariants。受影响的基因，转录和外显子以及已知的SNPs被存储在一个列表结构。看到
作者（S）----------Author(s)----------
Hans-Ulrich Klein
参见----------See Also----------
AnnotatedVariants-class, AVASet-class,
AnnotatedVariants-class，AVASet-class
举例----------Examples----------
variants = data.frame(
start=c(106157528, 106154991,106156184),
end=c(106157528, 106154994,106156185),
chromosome=c("4", "4", "4"),
strand=c("+", "+", "+"),
seqRef=c("A", "ATAG", "---"),
seqMut=c("G", "----", "ATA"),
seqSur=c("TACAGAA", "TTTATAGATA", "AGC---TCC"),
stringsAsFactors=FALSE)
rownames(variants) = c("snp", "del", "ins")
## Not run: annotateVariants(variants)[＃运行：annotateVariants（变种）]
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 11:47:20
