regionsCoverage(htSeqTools)
regionsCoverage()所属R语言包：htSeqTools
Compute coverage on user specified genomic regions.
计算用户指定的基因组区域的覆盖。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
regionsCoverage computes coverage for user specified genomic regions.
regionsCoverage计算为用户指定的基因组区域的覆盖面。
gridCoverage evaluates the coverage on a regular grid with the same number of points for each region (facilitating further plotting, clustering etc).
gridCoverage评估与规则的网格点，为每个区域的相同数量（促进进一步策划，聚类等）的覆盖范围。
stdGrid standardized the coverage by diviging by the average or maximum coverage at each region.
stdGrid标准化diviging平均或最大的覆盖范围，在每个区域的覆盖。
用法----------Usage----------
regionsCoverage(chr, start, end, cover)
gridCoverage(cover)
stdGrid(cover, colname="maxCov")
参数----------Arguments----------
参数：chr
Vector with chromosome names.
向量与染色体的名字。
参数：start
Vector with start position. start>end indicates that region is on the negative strand.
向量与起始位置。 start>end表明该区域是负链。
参数：end
Vector with end position. start>end indicates that region is on the negative strand.
向量与结束位置。 start>end表明该区域是负链。
参数：cover
For regionsCoverage, cover is an object of class RleList with the genome-wide coverage (typically obtained by a previous call to coverage). For gridCoverage this is the coverage evaluated at user-specified regions, as returned by regionsCoverage. For stdGrid this is the coverage evaluated on a grid, as returned by gridCoverage.
regionsCoverage，cover是一个对象类RleList的全基因组的覆盖（通常是由以前的调用获得coverage）。 gridCoverage这是regionsCoverage返回用户指定的区域，评估的覆盖面。 stdGrid这是评估在电网覆盖，返回gridCoverage。
参数：colname
Name of the column in cover@viewsInfo to be used for the standardizing. Currently only "meanCov" and "maxCov" are implemented.
名称的cover@viewsInfo列要使用的规范。目前，只有"meanCov"和"maxCov"实施。
值----------Value----------
regionsCoverage returns a list with two components
regionsCoverage返回两个组件列表
参数：views
RleViewsList with coverage evaluated at specified regions. Orientation is always so that start<end, i.e. For most practical purposes, regions on the reverse strand will need to be inverted.
RleViewsList评估覆盖在指定的区域。取向总是那么<月底开始，即最实用的目的，反向链上的区域将需要倒。
参数：viewsInfo
SplitDataFrameList containing information about each peak (chromosome, strand, mean and maximum coverage).
SplitDataFrameList包含有关每个峰的信息（染色体，钢绞线，平均和最大覆盖）。
gridCoverage and stdGrid return an object of class gridCover. The slot cover is a matrix with the coverage evaluated on a grid of 500 equi-spaced points, whereas the slot viewsInfo is the same as that returned by regionsCoverage (see above). For regions between 100bp and 500bp long, a linear interpolation is used to evaluate the coverage on the 500 points grid. For regions less than 100bp long, NAs are returned.
gridCoverage和stdGrid类gridCover返回一个对象。槽cover是一个覆盖500等间隔点的网格评估矩阵，而插槽viewsInforegionsCoverage（见上文）返回的是相同的。长100个基点和500bp的区域之间，线性插值用于评估的500点的网格覆盖。小于100bp的长的区域，NAS返回。
方法----------Methods----------
Methods for regionsCoverage:
的方法regionsCoverage：
Evaluates the coverage cover at the genomic positions specified by chr, start, end.
评估覆盖coverchr指定的基因组的位置，start，end。
Methods for stdGrid:
的方法stdGrid：
Standardizes the coverage evaluated on a grid (typically, as returned by gridCoverage) by dividing by the mean or maximum coverage.
规范评价上（通常情况下，由gridCoverage返回）除以平均或最大覆盖的网格的覆盖面。
参见----------See Also----------
gridCover-class
gridCover-class
举例----------Examples----------
#See help(enrichedPeaks)[见（enrichedPeaks）]
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。
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发表于 2012-2-25 22:04:30
