getBestNeighbors(KEGGSOAP)
getBestNeighbors()所属R语言包：KEGGSOAP
Client-side interface to obtain the name of genes that are
客户端接口，以获得基因的名称
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Given a KEGG gene id, the functions query the KEGG Sequence Similarity Database (SSDB) for genes that are homologous to the target gene in other organisms. Genes that share an arbitrary threshold level of similarity determined by alignment of matching bases are termed homologous.
鉴于一个KEGG基因id，查询功能是同源的靶基因在其他生物的基因KEGG序列的相似度数据库（SSDB）。分享相似的任意对齐配套碱基确定的阈值水平的基因被称为同源。
用法----------Usage----------
get.best.best.neighbors.by.gene(genes.id, start, max.results)
get.best.neighbors.by.gene(genes.id, start, max.results)
getBestNeighbors(genes.id, start, max.results, what = c("best", "best_best"))
参数----------Arguments----------
参数：genes.id
genes.id a character string for the id used by KEGG to represent the gene of interest. The id normally consists of three letters followed by a colon and then several numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)
genes.id为KEGG代表感兴趣的基因所使用的ID的字符串。 ID通常由三个字母，后跟一个冒号，然后几个数字。这三个字母是由属名第一个字母和关注的有机体的学名的种名的前两个字母（如HSA：111智人）
参数：start
start an integer to indicate the location of the entry in the query results from which the results will be extracted and returned
start一个整数来表示条目的查询结果中的位置将被提取并返回结果
参数：max.results
max.results an integer to indicate the maximum number of entries that will be extracted from the query results and returned
max.results整数表示从查询结果将提取的最大条目数，并返回
参数：what
what a character string that can either be "best" or "best\_best" to indicate whether reciprocal homologous genes are sought
what字符串，可以是“最好”或“最佳\ _best”，表明是否寻求互惠的同源基因
Details
详情----------Details----------
A given gene may have several homologous genes across organisms. A query to SSDB will have a list of genes that are homologous to the target gene. start and max.results indicate where on the list to start and stop to extract data and return the results.
一个给定的基因可能有生物体之间的几个同源基因。一个查询SSDB将靶基因同源的基因，有一个列表。 start和max.results表示，名单上启动和停止提取数据并返回结果。
getBestNeighbors is a general function that queries the SSDB database and gets the results based on whether the query is for best or best best homologous relationships.
getBestNeighbors是一个通用函数查询SSDB数据库，并会根据查询是否是最好的或最好的最好的同源关系的结果。
值----------Value----------
The functions return a list of lists. Each sub-list contains data for a gene that is homologous to the target gene with the following elements:
函数返回一个列表。每个子列表中包含一个基因是包含下列元素的靶基因同源的数据：
参数：genes\_id1
a character string for the id of the target gene used to query for hologous genes
为id用来查询为hologous基因的靶基因的字符串
参数：genes\_id2
a character string for the id of the homologous gene found in another organism
为同源基因的ID字符串在另一生物体的发现
参数：sw\_score
an integer for Smith-Waterman score between genes\_id1 and genes\_id2
Smith-Waterman算法得分基因\ _id1和基因\ _id2之间的整数
参数：bit\_score
a numeric value for the bit score between genes\_id1 and genes\_id2
为数值之间的基因\ _id1和基因\ _id2位得分
参数：identity
a numeric value between 0 and 1 for the degree of identity between genes\_id1 and genes\_id2
基因\ _id1和基因\ _id2度之间的身份为0和1之间的数值
参数：overlap
an integer for the overlapping length between genes\_id1 and genes\_id2
基因\ _id1和基因\ _id2之间的重叠长度的整数
参数：start\_position1
an integer for the start position of the alignment in genes\_id1
在基因\ _id1对齐的起始位置的整数
参数：end\_position1
an integer for the end position of the alignment in genes\_id1
在基因\ _id1整数对齐的结束位置
参数：start\_position2
an integer for the start position of the alignment in genes\_id2
在基因\ _id2对齐的起始位置的整数
参数：end\_position2
an integer for the end position of the alignment in genes\_id2
在基因\ _id2整数对齐的结束位置
参数：best\_flag\_1to2
a boolean that is TRUE if genes\_id2 is the best neighbor gene of genes\_id1
一个布尔值，这是事实，如果基因\ _id2是最好的邻居基因，基因\ _id1
参数：best\_flag\_2to1
a boolean that is TRUE if genes\_id1 is also the best neighbor gene of genes\_id2
一个布尔值是TRUE，如果基因\ _id1也是最好的邻居基因的基因\ _id2
参数：definition1
a character string for the definition of genes\_id1
\ _id1基因的定义为字符串
参数：definition2
a character string for the definition of genes\_id2
\ _id2基因的定义为字符串
参数：length1
an integer for the amino acid length of the genes\_id1
\ _id1基因的氨基酸长度的整数
参数：length2
an integer for the amino acid length of the genes\_id2
\ _id2基因的氨基酸长度的整数
作者（S）----------Author(s)----------
Jianhua Zhang
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
bestGenes <- get.best.neighbors.by.gene("eco:b0002",1, 5)
bestBestGenes <- get.best.best.neighbors.by.gene("eco:b0002",1, 5)
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 23:03:09
