peakScoring(nucleR)
peakScoring()所属R语言包：nucleR
Peak scoring function
山顶的打分函数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Scores peaks detected with function peakDetection according the height and the sharpness of the peak. This function can be called automatically from peakDetection if score=TRUE.
分数峰与功能检测peakDetection根据峰的高度和清晰度。此功能可以自动从被称为peakDetection如果score=TRUE。
用法----------Usage----------
## S4 method for signature 'numeric'
peakScoring(peaks, data, threshold="25%")
## S4 method for signature 'list'
peakScoring(peaks, data, threshold="25%", mc.cores=1)
## S4 method for signature 'IRanges'
peakScoring(peaks, data, threshold="25%", weight.width=1, weight.height=1, dyad.length=38)
## S4 method for signature 'IRangesList'
peakScoring(peaks, data, threshold="25%", weight.width=1, weight.height=1, dyad.length=38, mc.cores=1)
参数----------Arguments----------
参数：peaks
The identified peaks resulting from peakDetection. Could be a numeric vector with the position of the peaks, or a IRanges object with the extended range of the peak. For both types, list support is implemented as a numeric list or a IRangesList
从peakDetection确定峰。可能是一个numeric向量与峰的位置，或IRanges峰的扩展范围的对象。对于这两种类型，列表支持实施numeric列表或IRangesList
参数：data
Data of nucleosome coverage or intensites.
核小体覆盖或intensites数据。
参数：threshold
The non-default threshold previously used in peakDetection function, if applicable. Can be given as a percentage string (i.e., "25%" will use the value in the 1st quantile of data) or as an absolute coverage numeric value (i.e., 20 will not look for peaks in regions without less than 20 reads (or reads per milion)).
非默认的threshold以前使用在peakDetection的功能，如适用。可以给出一个百分比的字符串（即"25%"会使用在data的1位数的值），或作为一个绝对的覆盖数值（即，20不会找峰不小于20的读取（或％畅想读））的区域。
参数：dyad.length
How many bases account in the nucleosome dyad for sharpness description. If working with NGS data, works best with the reads width value for single-ended data or the trim value given to the processReads function.
碱基占多少核小体在锐度描述的对子。如果工作农工商数据，最好用单端数据或trim值processReads函数读取宽度值。
参数：weight.height, weight.width
If the score is a range, the height and the widht score (coverage and fuzzynes) can be defined with different weigths with these parameters. See details.
如果得分是一个范围，高度和widht的得分（覆盖率和fuzzynes）可以定义这些参数的不同weigths。查看详情。
参数：mc.cores
If input is a list or IRangeList, and multiple cores support is available, the maximum number of cores for parallel processing
如果输入是一个list或IRangeList，多核心的支持是可用的，核心的并行处理的最大数量
Details
详情----------Details----------
This function scores each previously identified peak according its height and sharpness.
此功能评分每先前确定的高峰期，根据其高度和清晰度。
The height score tells how large is a peak, higher means more coverage or intensity, so better positioned nucleosome. This score is obtained by checking the observed peak value in a Normal distribution with the mean and sd of data. This value is between 0 and 1.
高度得分告诉是多么大的一个高峰，意味着更多的覆盖范围或强度更高，以便更好地定位核小体。这个分数是通过检查平均的的data SD在正态分布的观测峰值。这个值是0和1之间。
The width score is a mesure of how sharp is a peak. With a NGS coverage in mind, a perfect phased (well-positioned) nucleosome is this that starts and ends exactly in the same place many times. The shape of this ideal peak will be a rectangular shape of the lenght of the read. A wider top of a peak could indicate fuzzyness. The parameter dyad.length tells how long should be the "flat" region of an ideal peak. The optimum value for this parameter is the lenght of the read in single-ended data or the trim value of the function processReads. For Tiling Array, the default value should be fine. This score is obtained calculating the ratio between the mean of the nucleosome scope (the one provided by range in the elements of peaks) and the dyad.length central bases. This value is normalized between 0 and 1.
宽度得分mesure是一个多么尖锐的是一个高峰。一个完美的阶段性（定位）核小体用一记农工商覆盖，这是开始和结束恰好在同一个地方多次。这个理想的峰的形状读取的长度将是一个长方形。可以表明fuzzyness广泛顶部的一个高峰。参数dyad.length告诉多久，应该是一个理想的高峰区域的“扁平化”。此参数的最佳值是在单端数据读取的长度或trim功能processReads价值。平铺阵列，默认值应该罚款。得到这个分数计算之间的核小体范围内的平均比例（范围提供一个在peaks元素）和dyad.length中央碱基。此值归0和1之间。
For punctual, single points peaks (provided by numeric vector or list as peaks attribute) the score returned is the height score.
对于守时，单点峰（numericpeaks属性向量或列表）返回的比分是高得分。
For range peaks the weighted sum of the heigth and width scores is used. This is: ((score.heigh * weigth.height) / sum.wei) + ((score.width * weigth.widht) / sum wei). Note that you can query for only one score by weting its weight to 1 and the other to 0.
范围peaks身高和宽度分数加权求和使用。这就是：((score.heigh * weigth.height) / sum.wei) + ((score.width * weigth.widht) / sum wei)。请注意，您可以查询只有一个得分weting其重量为1，其他为0。
值----------Value----------
In the case of numeric input, the value returned is a data.frame containing a 'peak' and a 'score' column. If the input is a list, the result will be a list of data.frame.
在numeric输入的情况下，返回的值是data.frame含有“峰”和“得分”列。如果输入的是list，结果将是一个listdata.frame。
If input is a IRanges or IRangesList, the result will be a RangedData object with one or multiple spaces respectively and a data column with the score.
如果输入是一个IRanges或IRangesList，结果将是一个RangedData对象分别与一个或多个空格和一个得分的数据列。
作者（S）----------Author(s)----------
Oscar Flores <a href="mailto flores@mmb.cpb.ub.es">oflores@mmb.cpb.ub.es</a>
参见----------See Also----------
peakDetection, processReads,
peakDetection，processReads
举例----------Examples----------
#Generate a synthetic map[生成一个合成的图]
map = syntheticNucMap(nuc.len=40, lin.len=130) #Trimmed length nucleosome map[修剪长度核小体图]
#Get the information of dyads and the coverage[获取信息的二元关系和覆盖]
peaks = c(map$wp.starts, map$fz.starts)
cover = filterFFT(coverage(map$syn.reads))
#Calculate the scores[计算分数]
scores = peakScoring(peaks, cover)
plotPeaks(scores$peak, cover, scores=scores$score, start=5000, end=10000)
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 2012-2-26 07:55:15
