dba.report(DiffBind)
dba.report()所属R语言包：DiffBind
Generate a report for a differential binding affinity analysis
产生一个差的亲和力分析报告
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates a report for a differential binding affinity analysis
生成的差的亲和力分析的报告
用法----------Usage----------
dba.report(DBA, contrast=1, method=DBA$config$AnalysisMethod,
th=.1, bUsePval=FALSE, fold=0, bNormalized=TRUE,
bCalled=FALSE, bCounts=FALSE, bCalledDetail=FALSE,
file,initString=DBA$config$reportInit,ext='csv',
bRangedData=DBA$config$RangedData)
参数----------Arguments----------
参数：DBA
DBA object. A differential binding affinity analysis needs to have been previously carried out (see dba.analyze).
DBA的对象。一个差亲和力分析需要，此前已进行了（见dba.analyze）。
参数：contrast
contrast number to report on. See dba.show(DBA, bContrast=T) to get contrast numbers.
数量对比报告。看到dba.show（DBA的，bContrast = T）对比数字。
参数：method
method used for analysis:
用于分析的方法：
DBA_EDGER
DBA_EDGER
DBA_DESEQ
DBA_DESEQ
DBA_EDGER_BLOCK
DBA_EDGER_BLOCK
参数：th
significance threshold; all sites with FDR (or p-values, see bUsePval) less than or equal to this value will be included in the report. A value of 1 will include all binding sites in the report.
意义的阈值;与FDR的所有网站（或p值，见bUsePval）小于或等于该值将包含在报告中。值1会在报告中包含的所有结合位点。
参数：bUsePval
logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.
逻辑指示是否使用阈值FDR（FALSE）或P-值（true）。
参数：fold
only sites with an absolute Fold value greater than equal to this will be included in the report.
只有一个绝对的折值大于等于这个网站将被列入报告中。
参数：bNormalized
logical indicating that normalized data (using normalization factors computed by differential analysis method) should be reported. FALSE uses raw count data.
逻辑表明，规范化的数据（使用差分析方法计算标准化的因素），应当报。假使用原始计数数据。
参数：bCalled
logical indicating that peak caller status should be included (if available from a previous call to dba.count(bCalledMasks=TRUE)). This will add a column for each group, each indicating the number of samples in the group identified as a peak in the original peaksets.
应包括逻辑表明，峰来电状态（从以前的的呼叫dba.count（bCalledMasks = TRUE，如果可用））。这将增加每个组列，每个显示的样本中作为原peaksets高峰期确定组数。
参数：bCounts
logical indicating that count data for individual samples should be reported as well as group statistics. Columns are added for each sample in the first group, followed by columns for each sample in the second group.
逻辑表明，个别样品的数量以及组统计报告的数据应。每个样品，每个样品列在第二组，第一组列添加。
参数：bCalledDetail
logical indicating that peak caller status should be included for each sample (if available). Columns are added for each sample in the first group, followed by columns for each sample in the second group.
逻辑表明，峰来电状态，应包括对每一个样品（如果可用）。每个样品，每个样品列在第二组，第一组列添加。
参数：file
if present, also save the report to a comma separated value (csv) file, using this filename.
如果存在，还保存报告到一个逗号分隔值（CSV）文件，这个文件名。
参数：initString
if saving to a file, pre-pend this string to the filename.
如果保存到一个文件，预PEND这个字符串的文件名。
参数：ext
if saving to a file, append this extension to the filename.
如果保存到一个文件，这个扩展追加到文件名。
参数：bRangedData
logical indicating whether the report should be returned as a RangedData object. Can be set as default behavior by setting DBA$config$RangedData=TRUE.
逻辑说明该报告是否应返回作为RangedData对象。设置DBA的美元配置$ RangedData = TRUE，可以设置为默认的行为。
值----------Value----------
A report dataframe or RangedData object, with a row for each binding site within the thresholding parameters, and the following columns:
一个报告dataframe的或RangedData对象，与行内的每个结合位点的阈值参数，下面列：
参数：Chr
Chromosome of binding site
结合位点的染色体
参数：Start
Starting base position of binding site
起始结合位点的基础地位
参数：End
End base position of binding site
年底结合位点的基础地位
参数：Conc
Concentration – mean (log) reads across all samples in both groups
两组读取所有样品浓度 - 意味着（log）
参数：Conc_group1
Group 1 Concentration – mean (log) reads across all samples first group
读取所有样本第一组第1组的浓度 - 均值（log）
参数：Conc_group2
Group 2 Concentration – mean (log) reads across all samples in second group
所有样品在第二组第2组浓度 - 均值（log）读取
参数：Fold
Fold difference – mean fold difference of binding affinity of group 1 over group 2 (Conc1 - Conc2). Absolute value indicates magnitude of the difference, and sign indicates which one is bound with higher affinity, with a positive value indicating higher affinity in the first group
倍的差异 - 意味着倍，超过第2组的第1组亲和力（Conc1 - Conc2）的差异。绝对值表示幅度的差异，和迹象表明哪一个必然具有较高的亲和力，以积极的指示在第一组的亲和力较高的价值，
参数：p-value
p-value calculation – statistic indicating significance of difference (likelihood difference is not attributable to chance)
P-值计算 - 统计显示差异显着性（可能性的区别是不可归责机会）
参数：FDR
adjusted p-value calculation – p-value subjected to multiple-testing correction
调整后的P-值计算 - p值受到多个测试校正
If bCalled is TRUE and caller status is available, two more columns will follow:
，如果bCalled是TRUE和呼叫者的状态是，两列如下：
参数：Called1
Number of samples in group 1 that identified this binding site as a peak
号码在第1组样品，此结合位点确定为高峰
参数：Called2
Number of samples in group 2 that identified this binding site as a peak
号码在第2组样品，此结合位点确定为高峰
If bCounts is TRUE, a column will be present for each sample in group 1, followed by each sample in group 2. The Sample ID will be used as the column header. This column contains the read counts for the sample.
如果bCounts为TRUE，列将目前每个样品每个样品2组，第1组。样品编号将用作列标题。此列包含只读样品计数。
If bCalledDetail is TRUE, a column will be present for each sample in group 1, followed by each sample in group 2. The Sample ID will be used as the column header. This column contains a "+" to indicate for which sites the sample was called as a peak, and a "-" if it was not so identified.
如果是TRUE bCalledDetail，一列将每个样品每个样品2组，1组。样品编号将用作列标题。此列包含一个“+”来表示网站的样本称为一个高峰，一个“ - ”如果它不那么确定。
作者（S）----------Author(s)----------
Rory Stark
举例----------Examples----------
data(tamoxifen_analysis)
#Retrieve DB sites with FDR < 0.1[FDR<0.1检索数据库网站]
tamoxifen.DB = dba.report(tamoxifen)
tamoxifen.DB
#Retrieve DB sites with p-value < 0.05 and Fold > 2[检索与p值DB网站<0.05折> 2]
tamoxifen.DB = dba.report(tamoxifen,th=.05,bUsePval=TRUE,fold=2)
tamoxifen.DB
#Retrieve all sites with confidence stats[找回信心的统计所有网站]
# and how many times each site was identified as a peak[和多少次被认定为每个站点一个高峰]
tamoxifen.DB = dba.report(tamoxifen, th=1, bCalled=TRUE)
tamoxifen.DB
#Retrieve all sites with confidence stats and normalized counts[找回信心的统计和规范化计数的所有网站]
tamoxifen.DB = dba.report(tamoxifen,th=1,bCounts=TRUE)
tamoxifen.DB
#Retrieve all sites with confidence stats and raw counts[找回信心的统计和原始计数的所有网站]
tamoxifen.DB = dba.report(tamoxifen,th=1,bCounts=TRUE,bNormalized=FALSE)
tamoxifen.DB
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 2012-2-25 16:40:10
