R语言 annotate包 findNeighbors()函数中文帮助文档(中英文对照)

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findNeighbors(annotate)
findNeighbors()所属R语言包：annotate

                                        A function to locate neighboring genes within a defined range
                                         函数定义的范围内找到邻近的基因

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Give a data package with mappings between Entrez Gene IDs and their locations on chromosomes, this function locates genes that are within a defined range on a given chromosome. If a Entrez Gene ID is passed as one of the arguments, genes located will be neighbors to the gene represented by the Entrez Gene ID within a defined range on the chromosome the target gene resides
号染色体上，这一功能定位的定义范围内某一染色体上的基因，Entrez基因标识和它们的位置之间的映射给一个数据包。如果一个Entrez基因ID作为一个参数传递，基因位于Entrez基因ID代表目标基因所在的染色体上的定义范围内的基因是邻居


用法----------Usage----------


findNeighbors(chrLoc, llID, chromosome, upBase, downBase, mergeOrNot = TRUE)
checkArgs(llID, chromosome, upBase, downBase)
findChr4LL(llID, chrEnv, organism)
getValidChr(organism)
getBoundary(loc, base, lower = TRUE)
weightByConfi(foundLLs)



参数----------Arguments----------

参数：chrLoc
chrLoc a character string for the name of the data package that contains mappings between Entrez Gene IDs and their locations on chromosomes. For each chromosome, there assumed to be mappings for the start and end locations of genes represented by Entrez Gene IDs. The data package needs to be built using chrLocPkgBuilder of AnnBuilder
chrLoc一个数据包，其中包含Entrez基因ID和其在染色体上的位置之间的映射的名称字符串。对于每一个染色体，假设是Entrez基因标识所代表的基因的起始和结束位置的映射。数据包需要使用AnnBuilder chrLocPkgBuilder


参数：llID
llID a character string for the Entrez Gene ID representing a gene whose neighbors are sought. llID can be missing
llIDEntrez基因身份证代表一个基因的邻居正在寻求字符串。 LLID可以被失踪


参数：chromosome
chromosome a character string for the number of the chromosome of interest. chromosome is only required for locating genes within a range on the chromosome
chromosome利益染色体数目的字符串。只需要在一定范围内定位在染色体上的基因染色体


参数：upBase
upBase a numeric or character string for the number of base pairs that defines the upper limit of the range to locate genes. If neighbors of a given gene is sought, the value will be the distance in number of base pairs from the target gene upstream, to which search for genes will be conducted. Otherwise, the value will be the upper limit in number of base pairs from the p arm, to which search for genes will be conducted
upBase一个数字或字符串的定义范围的上限，以找到基因的碱基对数目。如果对一个特定基因的邻居们的追捧，该值将是碱基对数量的靶基因上游的距离，将进行搜索的基因。否则，这个值将会从P组碱基对数量的上限，将进行基因搜索


参数：downBase
downBase a numeric or character string for the number of base pairs that defines the lower limit of the range to locate gene. If neighbors of a given gene is sought, the value will be the distance in number of base pairs from the target gene downstream, to which search for genes will be conducted. Otherwise, the value will be the lower limit in number of base pairs from the p arm, to which search for genes will be conducted
downBase一个数字或字符串的定义范围的下限，以找到基因的碱基对数目。如果对一个特定基因的邻居们的追捧，价值将是从下游的靶基因中的碱基对数量的距离，将进行搜索的基因。否则，该值将在从P组碱基对数量的限制，将进行基因搜索


参数：organism
organism a character string for the name of the organism of interest
organism利益的有机体的名称的字符串


参数：chrEnv
chrEnv an environment object with keys for Entrez Gene IDs and values for the chromosomes where genes reside
chrEnv环境与Entrez基因ID和价值观的键对象为在基因位于染色体


参数：loc
loc a numeric of character string for the chromosomal location of gene of interest
loc数字字符串感兴趣的基因的染色体定位


参数：base
base either a downBase or upBase
base或者downBase或upBase


参数：lower
lower a boolean indicating whether the lower or upper boundary of search limit is sought
lower一个布尔值，指示是否搜索限制或上，下边界要求


参数：mergeOrNot
mergeOrNot a boolean to indicate whether gene found up and down streams will be merged (TRUE)
mergeOrNot一个布尔值，指示是否发现基因上下游将合并（真）


参数：foundLLs
foundLLs a vector of character strings for Entrez Gene IDs
foundLLsEntrez基因ID的字符串矢量


Details

详情----------Details----------

A chrLoc data package can be created using function chrLocPkgBuilder of AnnBuilder, in which Entrez Gene IDs are mapped to location data on individual chromosomes.
可以创建一个数据包chrLoc使用功能AnnBuilder，在Entrez基因标识映射到单个染色体上的位置数据chrLocPkgBuilder。

Genes are considered to be neighbors to a given target gene or within a given range when the transcription of genes start and end within the given range.
基因被认为是一个给定的范围内的邻居，一个给定的目标基因或基因的转录时，给定的范围内开始和结束。

findNeighbors, checkArgs, findChr4LL, getValidChr, and getBoundary are accessory functions called by findNeighbors and may not have real values outside.  
findNeighbors，checkArgs，findChr4LL，getValidChr，并getBoundary的是由findNeighbors称为附件的功能，可能不会有真正的价值外。


值----------Value----------

The function returns a list of named vectors. The length of the list is one when genes in a given region are sought but varies depending on whether a given gene can be mapped to one or more chromosomes when neighboring genes of a target gene are sought. Names of vector can be "Confident" when a gene can be confidently placed on a chromosome or "Unconfident" when a gene can be placed on a chromosome but its exact location can not be determined with great confidence.
该函数返回一个命名为向量的名单。列表的长度是一个在某一特定区域的基因追捧，但不同取决于是否可以映射到一个或多个染色体的一个特定基因时寻求邻近的靶基因的基因。向量的名称可以是“有信心”时，一个基因可以自信地放置在一条染色体上或“不自信”，当一个基因可以被放置在一条染色体上，但其确切位置，不能以极大的信心决心。


作者（S）----------Author(s)----------


Jianhua Zhang



参考文献----------References----------

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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