R语言 DiffBind包 dba.overlap()函数中文帮助文档(中英文对照)

loveR

dba.overlap(DiffBind)
dba.overlap()所属R语言包：DiffBind

                                         Compute binding site overlaps (occupancy analysis)
                                         计算结合位点重叠（占用分析）

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Computes binding overlaps and co-occupancy statistics
计算约束力的重叠和共同占用统计


用法----------Usage----------


dba.overlap(DBA, mask, mode=DBA_OLAP_PEAKS, minVal=0,
            contrast, method=DBA$config$AnalysisMethod, th=.1, bUsePval=FALSE,
            report, byAttribute, bCorOnly=TRUE, CorMethod="pearson",
            bRangedData=DBA$config$RangedData)



参数----------Arguments----------

参数：DBA
DBA object  
DBA的对象


参数：mask
mask or vector of peakset numbers indicating a subset of peaksets to use (see dba.mask). When generating overlapping/unique peaksets, either two or three peaksets must be specified. If the mode type is DBA_OLAP_ALL, and a contrast is specified, a value of TRUE (mask=TRUE) indicates that all samples should be included (otherwise only those present in one of the contrast groups will be included).  
面罩或矢量的数字表明peakset的peaksets子集来使用（见dba.mask）。当产生重叠/独特peaksets，两个或三个peaksets必须指定。如果是DBA_OLAP_ALL模式类型，并指定了对比，一个TRUE值（MASK = TRUE）表明，所有样品应包括：（否则只有那些在对比组之一，将被纳入）。


参数：mode
indicates which results should be returned (see MODES below). One of:   
表示结果应返回（见下面的模式）。之一：

DBA_OLAP_PEAKS  
DBA_OLAP_PEAKS

DBA_OLAP_ALL  
DBA_OLAP_ALL

DBA_OLAP_RATE  
DBA_OLAP_RATE


参数：minVal
minimum score value to be considered a "called" peak.  
最低分数值被认为是一个“所谓的”高峰期。


参数：contrast
contrast number to use. Only specified if contrast data is to be used when mode=DBA_OLAP_ALL. See dba.show(DBA, bContrast=T) to get contrast numbers.   
使用对比数。只有指定的对比数据是要使用时，模式= DBA_OLAP_ALL。看到dba.show（DBA的，bContrast = T）对比数字。


参数：method
if contrast is specified and mode=DBA_OLAP_ALL, use data from method used for analysis:   
相反，如果是指定的模式= DBA_OLAP_ALL，使用用于分析数据方法：

DBA_EDGER  
DBA_EDGER

DBA_DESEQ  
DBA_DESEQ

DBA_EDGER_BLOCK  
DBA_EDGER_BLOCK


参数：th
if contrast is specified and mode=DBA_OLAP_ALL, significance threshold; all sites with FDR (or p-values, see bUsePval) less than or equal to this value will be included. A value of 1 will include all binding sites, but only the samples included in the contrast.  
相反，如果是指定模式=，意义阈值DBA_OLAP_ALL;与FDR的所有网站（或p值，见bUsePval）小于或等于这个值将被纳入。如果值为1，将包括所有结合位点，但只样品中包括对比度。


参数：bUsePval
if contrast is specified and mode=DBA_OLAP_ALL, logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.  
相反，如果是指定的模式= DBA_OLAP_ALL，逻辑指示是否使用阈值FDR（FALSE）或P-值（true）。


参数：report
if contrast is specified and mode=DBA_OLAP_ALL, a report (obtained from dba.report) specifying the data to be used. If counts are included in the report (and a contrast is specified), the count data from the report will be used to compute correlations, rather than the scores in the global binding affinity matrix.  If report is present, the method, th, and bUsePval parameters are ignored.  
相反，如果是指定的模式= DBA_OLAP_ALL，一份报告（得到从dba.report）指定要使用的数据。如果罪名包括在报告中（指定了对比），从报告中的计数数据将用于计算的相关性，而不是比在全球的亲和力矩阵的分数。如果报告是目前，法，日，和bUsePval参数将被忽略。


参数：byAttribute
when computing co-occupancy statistics (DBA_OLAP_ALL), limit comparisons to peaksets with the same value for a specific attribute, one of:   
当计算合作占用统计（DBA_OLAP_ALL），限制比较peaksets相同的值与一个特定的属性，其中：

DBA_ID  
DBA_ID

DBA_TISSUE  
DBA_TISSUE

DBA_FACTOR  
DBA_FACTOR

DBA_CONDITION  
DBA_CONDITION

DBA_REPLICATE  
DBA_REPLICATE

DBA_CONSENSUS  
DBA_CONSENSUS

DBA_CALLER  
DBA_CALLER

DBA_CONTROL  
DBA_CONTROL


参数：bCorOnly
when computing co-occupancy statistics (DBA_OLAP_ALL), logical indicating that only correlations, and not overlaps, should be computed. This is much faster if only correlations are desired (e.g. to plot the correlations using dba.plotHeatmap).  
（DBA_OLAP_ALL）共同占用统计计算时，表明唯一的相关性，而不是重叠，应计算逻辑。这是更快，如果只需要关联（例如使用dba.plotHeatmap绘制相关）。


参数：CorMethod
when computing co-occupancy statistics (DBA_OLAP_ALL), method to use when computing correlations.  
（DBA_OLAP_ALL），共同占用统计计算时使用的方法计算相关时。


参数：bRangedData
logical indicating whether, if mode==DBA_OLAP_PEAKS, the peaksets should be returned as RangedData objects. Can be set as default behavior by setting DBA$config$RangedData=TRUE.  
逻辑表示的peaksets，如果模式== DBA_OLAP_PEAKS是否应作为RangedData对象返回。设置DBA的美元配置$ RangedData = TRUE，可以设置为默认的行为。


Details

详情----------Details----------

MODE: Generate overlapping/unique peaksets:
模式：生成重叠/独特peaksets：

dba.overlap(DBA, mask, mode=DBA_OLAP_PEAKS, minVal)
dba.overlap（DBA来说，面具，模式= DBA_OLAP_PEAKS，MINVAL）

MODE: Compute correlation and co-occupancy statistics (e.g. for dba.plotHeatmap):
模式：计算相关性和合作占用统计（如为dba.plotHeatmap）：

dba.overlap(DBA, mask, mode=DBA_OLAP_ALL, byAttribute, minVal, attributes, bCorOnly, CorMethod)
dba.overlap（DBA来说，面具，模式= DBA_OLAP_ALL，byAttribute，MINVAL，属性，bCorOnly，CorMethod）

MODE: Compute correlation and co-occupancy statistics using significantly differentially bound sites (e.g. for dba.plotHeatmap):
模式计算的相关性和合作占用统计显著差异必然的网站（例如为dba.plotHeatmap）：

dba.overlap(DBA, mask, mode=DBA_OLAP_ALL, byAttribute, minVal, contrast, method, th=, bUsePval, attributes, bCorOnly, CorMethod)
dba.overlap（DBA来说，面具，模式= DBA_OLAP_ALL，byAttribute，MINVAL，相比之下，方法，日，bUsePval，属性，bCorOnly，CorMethod）

Note that the scores from the global binding affinity matrix will be used for correlations unless a report containing count data is specified.
请注意，从全球的亲和力矩阵的分数将相关的使用，除非指定了一份报告，计数资料。

MODE: Compute overlap rates at different stringency thresholds:
模式：在不同的严格阈值计算重叠率：

dba.overlap(DBA, mask, mode=DBA_OLAP_RATE, minVal)
dba.overlap（DBA来说，面具，模式= DBA_OLAP_RATE，MINVAL）


值----------Value----------

Value depends on the mode specified in the mode parameter.
值取决于模式参数中指定的模式。

If mode = DBA_OLAP_PEAKS, Value is an overlap record: a list of three peaksets for an A-B overlap, and seven peaksets for a A-B-C overlap:
如果模式= DBA_OLAP_PEAKS，价值是重叠记录的AB重叠，并为ABC重叠七peaksets peaksets：


参数：inAll
peaks in all peaksets
峰所有peaksets的


参数：onlyA
peaks unique to peakset A
峰独特peakset一个的


参数：onlyB
peaks unique to peakset B
峰独特peakset乙的


参数：onlyC
peaks unique to peakset C
峰独特peaksetÇ


参数：notA
peaks in both peaksets B and C but not peakset A
在B和C都peaksets但不是的的山峰peakset一个


参数：notB
peaks in both peaksets A and C but not peakset B
峰在两个peaksets A和C，但不是peakset乙


参数：notC
peaks in both peaksets A and B but not peakset C
峰都peaksets A和B，但不peaksetÇ

If mode = DBA_OLAP_ALL, Value is a correlation record: a matrix with a row for each pair of peaksets and the following columns:
如果模式= DBA_OLAP_ALL，价值是一个相关记录：一排，每个peaksets对下列列的矩阵：


参数：A
peakset number of first peakset in overlap
在重叠第一peakset数peakset


参数：B
peakset number of second peakset in overlap
在重叠peakset第二peakset数


参数：onlyA
number of sites unique to peakset A
独特peakset一个网站数


参数：onlyB
number of sites unique to peakset B
peakset乙独特的网站数


参数：inAll
number of peaks in both peakset A and B (merged)
峰在两个peakset A和B的数量（合并）


参数：R2
correlation value A vs B
A对B的相关值


参数：Overlap
percentage overlap (number of overlapping sites divided by number of peaks unique to smaller peakset
百分比重叠（重叠的站点数除以独特的小peakset峰

If mode = DBA_OLAP_RATE, Value is a vector whose length is the number of peaksets, containing the number of overlapping peaks at the corresponding minOverlaps threshold (i.e., Value[1] is the total number of unique sites, Value[2] is the number of unique sites appearing in at least two peaksets, Value[3] the number of sites overlapping in at least three peaksets, etc.).
如果模式= DBA_OLAP_RATE，价值是一个向量，其长度是数peaksets，包含在相应的阈值minOverlaps叠嶂的数量（即[1]的价值是独特的网站总数，价值[2]是数独特的网站出现在至少两个peaksets，价值[3]重叠至少有三个peaksets，等等）的网站数量。


作者（S）----------Author(s)----------



Rory Stark




举例----------Examples----------


data(tamoxifen_peaks)
# default mode: DBA_OLAP_PEAKS -- get overlapping/non overlapping peaksets[默认模式：DBA_OLAP_PEAKS  - 重叠/非重叠peaksets]
mcf7 = dba.overlap(tamoxifen,tamoxifen$masks$MCF7)
names(mcf7)
mcf7$inAll

# mode:  DBA_OLAP_ALL -- get correlation record[模式：DBA_OLAP_ALL  - 获取相关记录]
mcf7 = dba(tamoxifen,tamoxifen$masks$MCF7)
mcf7.corRec = dba.overlap(mcf7,mode=DBA_OLAP_ALL,bCorOnly=FALSE)
mcf7.corRec

# mode: DBA_OLAP_RATE -- get overlap rate vector[模式：DBA_OLAP_RATE  - 获得重叠率向量]
data(tamoxifen_peaks)
rate = dba.overlap(tamoxifen, mode=DBA_OLAP_RATE)
rate
plot(rate,type='b',xlab="# peaksets",ylab="# common peaks",[peaksets“，ylab =”＃共同峰“]
     main="Tamoxifen dataset overlap rate")

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。