predictCoding(VariantAnnotation)
predictCoding()所属R语言包：VariantAnnotation
Predict amino acid coding changes for variants
预测编码氨基酸的变异变化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Predict amino acid coding changes for variants that fall in a coding region.
预测氨基酸编码在编码区的变种变化。
用法----------Usage----------
## S4 method for signature 'GRanges,GRangesList,ANY,character'
predictCoding(query, subject,
seqSource, varAllele, ...)
参数----------Arguments----------
参数：query
A Ranges or GRanges instance containing the variants to be annotated. If a Ranges instance is provided it will be coerced to a GRanges.
一个范围或农庄实例包含变种注明的。如果一个范围的实例将被强制到一个农庄。
参数：subject
A GRangesList or a TranscriptDb instance. When subject is provided as a GRangesList it is assumed that it was created with the 'cdsBy' function on a TranscriptDb. If subject is a TranscriptDb, the coding regions will be identified using the 'cdsBy' function on this object.
一个GRangesList或TranscriptDb实例。当subject因为它被认为是与“cdsBy功能上TranscriptDb创建GRangesList提供。如果subject是一个TranscriptDb，编码区，将确定“cdsBy”功能，使用此对象。
参数：seqSource
A BSgenome instance or an FaFile to be used for sequence extraction.
一个BSgenome实例或FaFile序列提取使用。
参数：varAllele
A character representing the name of the column in query that contains the variant alleles. The data in the column should be a DNAStringSet. Insertions and deletions are represented by a missing value.
一个字符代表query，列的名称中包含的变异基因。列中的数据应该是一个DNAStringSet。插入和删除缺失值表示。
参数：...
Additional arguments
额外的参数
Details
详情----------Details----------
Reference sequences are extracted from fasta files or a BSgenome based on the ranges specified in the query. Variant alleles provided in the varAllele argument are substituted into the reference sequences and transcribed. Variant sequences are transcribed only if the substitution, insertion or deletion results in a new sequence length divisible by 3.
参考序列中提取FASTA文件或对在query指定的范围根据BSgenome。 varAllele参数代入变异等位基因的参考序列和转录。变异序列的转录只有在一个新的序列的长度被3整除的替换，插入或删除的结果。
值----------Value----------
A DataFrame of variants that fall within a coding region. Each row represents a variant-transcript match. If a variant matched multiple transcripts, multiple rows are returned for the variant.
编码区范围内的变种DataFrame。每一行代表一个变种成绩单比赛。如果的变种匹配多个成绩单，返回多行的变种。
Columns include queryHits, txID, refSeq, varSeq, refAA, varAA, Consequence, and any metadata that was present in the subject. queryHits provides a map to the variants in the original query. refSeq and varSeq contain the reference and variant-modified DNA sequences. Reference and variant amino acid codes are provided in refAA and varAA. Variant sequences are transcribed only if the substitution, insertion or deletion results in a new sequence length divisible by 3. When a sequence is not transcribed the varAA column is empty and the variant is classified as a frameshift in the Consequence column. Possible values for Consequence are synonymous, nonsynonymous, or frameshift. See the vignette for more details.
列包括queryHits，txID，refSeq，varSeq，refAA，varAA，Consequence，任何元数据，是目前在subject。 queryHits提供了一个图在原query的变种。 refSeq和varSeq包含的参考和变种修改后的DNA序列。在refAA和varAA提供参考和变异氨基酸代码。变异序列的转录只有在一个新的序列的长度被3整除的替换，插入或删除的结果。当一个序列不是转录varAA列是空的，和Consequence列移列为变种。 Consequence可能的值是同义，同义，或移。看到更多细节的小插曲。
作者（S）----------Author(s)----------
Michael Lawrence and Valerie Obenchain
参见----------See Also----------
locateVariants getTranscriptSeqs
locateVariants getTranscriptSeqs
举例----------Examples----------
library(TxDb.Hsapiens.UCSC.hg18.knownGene)
library(BSgenome.Hsapiens.UCSC.hg18)
data(variants)
txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene
aaCoding <- predictCoding(variants, txdb, seqSource=Hsapiens,
varAllele="varAllele")
# TODO : example for fasta[TODO：在此例为FASTA]
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 15:57:21
