getOverlaps(segmentSeq)
getOverlaps()所属R语言包：segmentSeq
Identifies overlaps between two sets of genomic coordinates
标识两套基因组坐标之间的重叠
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function identifies which of a set of genomic segments overlaps with another set of coordinates; either with partial overlap or with the segments completely contained within the coordinates. The function is used within the "segmentSeq" package for various methods of constructing a segmentation map, but may also be useful in downstream analysis (e.g. annotation analyses).
此功能可识别的一组重叠的基因片段与另一组坐标;部分重叠或完全在坐标中的段。该函数用于在segmentSeq建设分割图的各种方法包，但也有可能在下游分析有用（例如注解分析）。
用法----------Usage----------
getOverlaps(coordinates, segments, overlapType = "overlapping", whichOverlaps = TRUE, cl)
参数----------Arguments----------
参数：coordinates
A GRanges object defining the set of coordinates with which the segments may overlap.
一个GRanges对象定义一套与该段可能重叠的坐标。
参数：segments
A GRanges object defining the set of segments which may overlap within the coordinates.
一个GRanges对象定义段内的坐标重叠。
参数：overlapType
Which kind of overlaps are being sought? Can be one of "overlapping", "contains" or "within". See Details.
正在寻求这种重叠？可以是一个“重叠”，“包含”或“内”。查看详细信息。
参数：whichOverlaps
If TRUE, returns the "segments" overlapping with the "coordinates". If FALSE, returns a boolean vector specifying which of the "coordinates" overlap with the "segments".
如果是TRUE，则返回“坐标”重叠的“分部”。如果为FALSE，返回一个布尔向量与“分部”指定的“坐标”重叠。
参数：cl
A SNOW cluster object, or NULL. See Details.
雪聚类对象，或NULL。查看详细信息。
Details
详情----------Details----------
If overlapType = "overlapping" then any overlap between the "coordinates" and the "segments" is sufficient. If overlapType = "contains" then a region defined in "coordinates" must completely contain at least one of the "segments" to count as an overlap. If overlapType = "within" then a region defined in "coordinates" must be completely contained by at least one of the "segments" to count as an overlap.
如果overlapType = "overlapping"之间的“坐标”和“分部”任何重叠充分。如果overlapType = "contains"然后在“坐标”定义的区域必须完全包含至少一个“分部”，算作重叠。如果overlapType = "within"然后在“坐标”定义的区域必须完全包含至少算作重叠的“分部”之一。
A 'cluster' object (package: snow) may usefully be used for parallelisation of this function when examining large data sets. Passing NULL to this variable will cause the function to run in non-parallel mode.
一个'cluster'对象（包雪）可能有效地用于此功能的并行化研究大型数据集时。这个变量传递NULL会导致在非并行模式运行的功能。
值----------Value----------
If whichOverlaps = TRUE, then the function returns a list object with length equal to the number of rows of the "coordinates" argument. The "i"th member of the list will be a numeric vector giving the row numbers of the "segments" object which overlap with the "i"th row of the "coordinates" object, or NA if no segments overlap with this coordinate region.
如果whichOverlaps = TRUE，那么该函数返回一个列表对象，长度等于行坐标的说法。 “列表中的第i个成员将是一个数值向量，给予行第i行段坐标的对象，或NA的对象重叠，如果没有段重叠这个坐标区域。
If whichOverlaps = FALSE, then the function returns a boolean vector with length equal to the number of rows of the "coordinates" argument, indicating which of the regions defined in coordinates have the correct type of overlap with the "segments".
如果whichOverlaps = FALSE，那么该函数返回一个布尔向量长度等于行坐标的说法，表示在坐标定义的区域有重叠的正确类型的“分部” 。
作者（S）----------Author(s)----------
Thomas J. Hardcastle
举例----------Examples----------
# Define the chromosome lengths for the genome of interest.[定义感兴趣的基因组染色体长度。]
chrlens <- c(2e6, 1e6)
# Define the files containing sample information.[定义文件包含样本信息。]
datadir <- system.file("extdata", package = "segmentSeq")
libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")
# Establish the library names and replicate structure.[建立图书馆的名称和复制结构。]
libnames <- c("SL9", "SL10", "SL26", "SL32")
replicates <- c(1,1,2,2)
# Process the files to produce an `alignmentData' object.[处理文件，以生产alignmentData“对象。]
alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
replicates, libnames = libnames, chrs = c(">Chr1", ">Chr2"), chrlens =
chrlens, gap = 100)
# Find which tags overlap with an arbitrary set of coordinates.[查找任意设置一个坐标重叠的标签。]
getOverlaps(coordinates = GRanges(seqnames = c(">Chr1"),
IRanges(start = c(1,100,2000), end = c(40,3000,5000))),
segments = alignData@alignments, overlapType = "overlapping",
whichOverlaps = TRUE, cl = NULL)
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 2012-2-26 13:59:56
