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

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

                                         Count reads in binding site intervals
                                         计数读取的结合位点间隔

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Counts reads in binding site intervals
计数读取的结合位点间隔


用法----------Usage----------


dba.count(DBA, peaks, minOverlap=2, score=DBA_SCORE_READS_MINUS, bLog=FALSE,
          insertLength, minMaxval, bCalledMasks=TRUE,
          bCorPlot=TRUE, bParallel=DBA$config$RunParallel)



参数----------Arguments----------

参数：DBA
DBA object  
DBA的对象


参数：peaks
RangedData or matrix containing intervals to use. If missing, generates a consensus peakset using minOverlap parameter.  
RangedData或矩阵包含的时间间隔使用。如果丢失，产生一个共识peakset使用minOverlap参数。


参数：minOverlap
only include peaks in at least this many peaksets when generating consensus peakset (i.e. when peaks parameter is missing).  
只包括至少这许多peaksets，峰时，产生共识peakset的时（即缺少高峰参数时）。


参数：score
which score to use in the binding affinity matrix. Note that all raw read counts are maintained for use by dba.analyze, regardless of how this is set. One of:   <table summary="Rd table"> <tr>  <td align="left"> DBA_SCORE_RPKM </td><td align="left"> RPKM for interval using only reads from ChIP</td> </tr> <tr>  <td align="left"> DBA_SCORE_RPKM_FOLD </td><td align="left"> RPKM for interval from ChIP divided by RPKM for interval from control</td> </tr> <tr>  <td align="left"> DBA_SCORE_READS </td><td align="left"> raw read count for interval using only reads from ChIP</td> </tr> <tr>  <td align="left"> DBA_SCORE_READS_FOLD </td><td align="left"> raw read count for interval from ChIP divided by read count for interval from control</td> </tr> <tr>  <td align="left"> DBA_SCORE_READS_MINUS </td><td align="left"> raw read count for interval from ChIP minus read count for interval from control</td> </tr> <tr>  <td align="left"> </td> </tr>  </table>  
其中得分亲和力矩阵使用。请注意，所有原料读取计数维持使用由dba.analyze，不论如何设置。其中：<table summary="Rd table"> <TR> <TD ALIGN="LEFT"> DBA_SCORE_RPKM </ TD> <td ALIGN="LEFT"> RPKM使用只读取从芯片间隔</ TD> </ TR> <TR> <td ALIGN="LEFT"> DBA_SCORE_RPKM_FOLD </ TD> <td ALIGN="LEFT"> RPKM从芯片由RPKM划分为间隔从控制间隔</ TD> </ TR> <TR> < TD对齐=“左”> DBA_SCORE_READS </ TD> <td ALIGN="LEFT">原料使用只读取从芯片读取间隔计数</ TD> </ TR> <TR> <td ALIGN="LEFT"> DBA_SCORE_READS_FOLD </ TD> <td ALIGN="LEFT">原料读通过读控制</ TD>间隔数除以间隔从芯片计数</ TR> <TR> <TD ALIGN="LEFT"> DBA_SCORE_READS_MINUS </ TD > <td ALIGN="LEFT">原料读取从芯片间隔数减去读计数的时间间隔为控制</ TD> </ TR> <TR> <TD ALIGN="LEFT"> </ TD> </ TR> </ TABLE>


参数：bLog
logical indicating whether log2 of score should be used (only applies to DBA_SCORE_RPKM_FOLD and DBA_SCORE_READS_FOLD).  
逻辑表示得分的log2是否应使用（只适用到DBA_SCORE_RPKM_FOLD和DBA_SCORE_READS_FOLD的）。


参数：insertLength
if present, this value will be used as the length of the reads.  Each read will be extended from its endpoint along the appropriate strand by this many bases.  If missing, the read size indicated in the BAM/SAM/BED file will be used.  
如果存在的话，这个值将被用作读取的长度。很多碱基以及相应的链将延长每次读从它的终点。如果错过，读的大小表示在BAM / SAM /床文件将被使用。


参数：minMaxval
value to use for filtering intervals with low read counts.  Only intervals where at least one sample has at least minMaxval reads will be included.  If missing, includes all intervals. If peaks is NULL, will remove sites from existing DBA object without recounting.  
值用于过滤与低阅读计数间隔。其中至少有一个样本至少有minMaxval读取仅间隔将包括在内。如果失踪，其中包括所有的时间间隔。如果峰是NULL，将删除从现有的DBA对象的网站，没有叙述。


参数：bCalledMasks
logical indicating whether to compute site masks for each peakset indicating which sites were originally identified as peaks(used by dba.report).   
逻辑表示是否计算每个peakset表明该网站最初被确定为峰（dba.report）的网站口罩。


参数：bCorPlot
logical indicating whether to plot a correlation heatmap for the counted data  
逻辑说明是否为计算数据绘制相关热图


参数：bParallel
if TRUE, use multicore to get counts for each read file in parallel  
如果为TRUE，使用多核每个并行读取文件数


值----------Value----------

DBA object with binding affinity matrix based on read count scores.
DBA根据读取数分数与亲和力矩阵对象。


作者（S）----------Author(s)----------



Rory Stark and Gordon Brown




举例----------Examples----------


# These won't run unless you have the reads available in a BAM, SAM, or BED file[这些将不会运行，除非你有在BAM，SAM或床上文件的读取]
data(tamoxifen_peaks)
## Not run: tamoxifen = dba.count(tamoxifen)[＃不运行：他莫昔芬= dba.count（三苯氧胺）]


# Count using a peakset made up of only peaks in all MCF7 replicates[指望用在所有的MCF7复制的唯一峰1 peakset]
data(tamoxifen_peaks)
mcf7Common = dba.overlap(tamoxifen,tamoxifen$masks$MCF7)
## Not run: tamoxifen = dba.count(tamoxifen,peaks=mcf7Common$inAll)[＃无法运行：他莫昔芬= dba.count（他莫昔芬，峰= mcf7Common美元inAll）]
tamoxifen

# Change binding affinity scores[更改亲和力分数]
data(tamoxifen_counts)
tamoxifen = dba.count(tamoxifen,peaks=NULL,score=DBA_SCORE_READS)
head(tamoxifen$vectors)
tamoxifen = dba.count(tamoxifen,peaks=NULL,score=DBA_SCORE_RPKM_FOLD)
head(tamoxifen$vectors)

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


注：
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