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

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boundingIndices(genoset)
boundingIndices()所属R语言包：genoset

                                        Find indices of features bounding a set of chromsome ranges/genes...
                                         包围了一套染色体范围/基因功能指数......

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Find indices of features bounding a set of chromsome ranges/genes
包围了一套染色体范围/基因功能指数


用法----------Usage----------





参数----------Arguments----------

参数：starts
integer vector of first base position of each query range
整数向量的每个查询范围的基础地位


参数：stops
integer vector of last base position of each query range
去年碱基的位置，每个查询范围的整数向量


参数：positions
Base positions in which to search
相应的职位，在其中搜索


参数：valid.indices
logical, TRUE assures that the returned indices don't go off either end of the array, i.e. 0 becomes 1 and n+1 becomes n
逻辑，TRUE确保返回的指数不熄灭数组的两端，即0变为1和n +1到n


参数：offset
integer, value to add to all returned indices. For the case where positions represents a portion of some larger array (e.g. a chr in a genome)
整数，值添加到所有返回的指数。对于此案的立场表示一些较大的阵列的一部分（例如，在一个基因组CHR）


参数：all.indices
logical, return a list containing full sequence of indices for each query
逻辑，返回一个列表，其中包含全序列指数为每个查询


Details

详情----------Details----------

This function is similar to findOverlaps but it guarantees at least two features will be covered. This is useful in the case of finding features corresponding to a set of genes. Some genes will fall entirely between two features and thus would not return any ranges with findOverlaps. Specifically, this function will find the indices of the features (first and last) bounding the ends of a range/gene (start and stop) such that first <= start < stop <= last. Equality is necessary so that multiple conversions between indices and genomic positions will not expand with each conversion. Ranges/genes that are outside the range of feature positions will be given the indices of the corresponding first or last index rather than 0 or n + 1 so that genes can always be connected to some data.
这种功能类似findOverlaps的，但它保证至少有两个功能将被覆盖。这是在寻找相应的一组基因功能的情况下非常有用。有些基因会完全落在两个功能之间，因此不会返回与findOverlaps任何范围。具体来说，此功能将找到的功能边界的两端（第一个和最后一个）指数范围/基因（启动和停止），这样第一页<=开始停止<=最后。平等是必要的，因此，指数和基因组的位置之间的多次转换会不会扩大相互转换。范围/基因特征位置的范围以外的，将给予相应的第一个或最后一个索引，而不是0或n + 1的指标，使基因总是可以被连接到的一些数据。

This function uses some tricks from findIntervals, where is for k queries and n features it is O(k * log(n)) generally and ~O(k) for sorted queries. Therefore will be dramatically faster for sets of query genes that are sorted by start position within each chromosome. The index of the stop position for each gene is found using the left bound from the start of the gene reducing the search space for the stop position somewhat. This function has important differences from intervalBound, which uses findInterval: boundingIndices does not check for NAs or unsorted data in the subject positions. Also, the positions are kept as integer, where intervalBound (and findInterval) convert them to doubles. These three once-per-call differences account for much of the speed improvement in boundingIndices. These three differences are meant for position info coming from GenoSet objects and boundingIndices2 is safer for general use. boundingIndices works on integer postions and does not check that the positions are ordered. The starts and stops need not be sorted, but
此功能从findIntervals使用的一些技巧，k查询和n功能是O（K *log（n））一般~O（K）排序查询。因此将极大地加快查询的基因集在每个染色体的位置开始排序。被发现使用从基因开始减少搜索空间的停止位置有点约束的左边的每一个基因的停止位置的索引。此功能具有重要的区别：从intervalBound，它使用findInterval不检查boundingIndices NAS或无序数据中的主体地位。此外，位置保持为整数，其中intervalBound（及findInterval），并将其转换为双打。每一次呼叫这三个差异的帐户，速度boundingIndices改善多。这三个差异意味着来自GenoSet对象的位置信息和boundingIndices2是一般用途安全。的boundingIndices整数志愿服务岗位上工作，不检查的立场是有序的。启动和停止不需要进行排序，但


值----------Value----------

integer matrix of 2 columms for start and stop index of range in data or a list of full sequences of indices for each query (see all.indices argument)
整数矩阵（见all.indices参数）2，启动和停止数据范围的指数或指数为每个查询的序列列表columms


作者（S）----------Author(s)----------


Peter M. Haverty <a href="mailto:phaverty@gene.com">phaverty@gene.com</a>



参见----------See Also----------

boundingIndices2
boundingIndices2


举例----------Examples----------



转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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