getSequence(biomaRt)
getSequence()所属R语言包：biomaRt
Retrieves sequences
获取序列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function retrieves sequences given the chomosome, start and end position or a list of identifiers. Using getSequence in web service mode (default) generates 5' to 3' sequences of the requested type on the correct strand. The type of sequence returned can be specified by the seqType argument which takes the following values: 'cdna';'peptide' for protein sequences;'3utr' for 3' UTR sequences,'5utr' for 5' UTR sequences; 'gene\_exon' for exon sequences only; 'transcript\_exon\_intron' gives the full unspliced transcript, that is exons + introns;'gene\_exon\_intron' gives the exons + introns of a gene;'coding' gives the coding sequence only;'coding\_transcript\_flank' gives the flanking region of the transcript including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute;'coding\_gene\_flank' gives the flanking region of the gene including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute; 'transcript\_flank' gives the flanking region of the transcript exculding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute; 'gene\_flank' gives the flanking region of the gene excluding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute.
此函数检索chomosome，开始和结束位置或标识符的列表的序列。使用，某个getSequence Web服务模式（默认），产生5至3序列正确的链上的请求类型。返回的序列类型可以由指定的seqType参数需要以下值：“基因”，“肽”的蛋白质序列; 3 UTR的3UTR序列，5 UTR 5非编码区序列的基因\外显子序列_exon“;谈话\ _exon \ _intron”给予充分的未拼接的谈话，是外显子+内含子“基因\ _exon \ _intron使外显子+一个基因的内含子编码”给出的编码序列“编码\ _transcript \ _flank”给人的谈话内容包括非编码区的侧翼区域，必须伴随着一个上游或下游的属性值“编码\ _gene \ _flank”给出了该基因的侧翼区，包括非编码区，必须伴随着一个上游或下游的属性值;谈话\ _flank给侧翼区的exculding的非编码区的成绩单，这必须伴随着一个上游或下游的属性值;基因\ _flank给人不包括非编码区基因的侧翼区，必须伴随着与上游或下游的属性值。
用法----------Usage----------
getSequence( chromosome, start, end, id, type, seqType, upstream, downstream, mart, verbose=FALSE)
参数----------Arguments----------
参数：chromosome
Chromosome name
染色体的名字
参数：start
start position of sequence on chromosome
启动序列号染色体上的位置
参数：end
end position of sequence on chromosome
序列号染色体上的结束位置
参数：id
An identifier or vector of identifiers.
标识符标识符或向量。
参数：type
The type of identifier used. Supported types are hugo, ensembl, embl, entrezgene, refseq, ensemblTrans and unigene. Alternatively one can also use a filter to specify the type. Possible filters are given by the listFilters function
标识符类型使用。支持的类型是雨果，ENSEMBL，EMBL，entrezgene的RefSeq，ensemblTrans和Unigene。另外还可以使用一个过滤器来指定类型。可能滤波器由listFilters功能
参数：seqType
Type of sequence that you want to retrieve. Allowed seqTypes are: cdna, peptide, 3utr, 5utr, genomic
要检索的序列类型。允许seqTypes是：基因，多肽，3utr，5utr，基因组
参数：upstream
To add the upstream sequence of a specified number of basepairs to the output.
添加指定数量的碱基上游序列的输出。
参数：downstream
To add the downstream sequence of a specified number of basepairs to the output.
添加下游指定数量的碱基序列的输出。
参数：mart
object of class Mart created using the useMart function
沃尔玛类的对象创建使用useMart功能
参数：verbose
If verbose = TRUE then the XML query that was send to the webservice will be displayed.
如果VERBOSE = TRUE，那么将显示XML查询，发送到WebService。
作者（S）----------Author(s)----------
Steffen Durinck
举例----------Examples----------
if(interactive()){
mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart)
show(seq)
seq = getSequence(id="1939_at", type="affy_hg_u95av2", seqType="gene_flank",upstream = 20, mart = mart)
show(seq)
}
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 2012-2-25 13:34:09
