rnaither(RNAither)
rnaither()所属R语言包：RNAither
Wrapper function for full automated analysis
包装功能的全自动化分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs a standard analysis of the data (quality and statistics) from a dataset file.
执行标准的分析数据从一个数据集文件（质量和统计）。
用法----------Usage----------
rnaither(data, expname, excludeCellcounts="none", logtransform=FALSE, normalization=c("lowess","bscore"), test="ttest", scorethresh=2.0, pvalthresh=0.05, dogo=FALSE, outdir="results", layoutnames="NA", makeplots=TRUE, reorder=TRUE)
参数----------Arguments----------
参数：data
A data frame containing the experimental data to analyze. Each row is corresponding to one well, with the following columns:
一个数据框包含的实验数据来分析。每一行对应一个孔，与下面的列：
Spotnumber The position of the well on the plate
Spotnumber很好的位置上盘
Internal_GeneID The ID of the siRNA
Internal_GeneID的siRNA的ID
GeneName The gene name
GeneName的基因名称
SpotType Can be -1, 0, 1 or 2. Type -1 wells (e.g. emtpy wells, wells with poor quality) are not considered in subsequent analyses but are kept in the data set for the sake of completeness. Type 0 wells correspond to negative controls, type 1 wells to positive controls. Type 2 wells correspond to the standard data wells.
SpotType可以是-1，0，1或2。类型-1井（如emtpy井，井质量差）不认为在随后的分析，但在保持数据的完整性而设置的。 0型油井对应阴性对照，1型井阳性对照。 2型井对应的标准数据水井。
SigIntensity The signal intensity (channel 1)
SigIntensity信号强度（通道1）
SDSIntensity The standard deviation of the signal intensity, if available
SDSIntensity信号强度的标准差，如果有
Background The background per well, if available
背景背景每口井，如果有
LabtekNb The plate number
LabtekNb的车牌号码
RowNb The row number
RowNb的行数
ColNb The column number
ColNb的列数
ScreenNb The screen number
ScreenNb的屏幕数量
NbCells E.g. the number of cells identified in the well (channel 2)
NbCells例如以及确定单元的数量（通道2）
PercCells The ratio (number of identified cells)/(number of identified objects)
PercCells的比例（确定单元数）/（鉴定对象的数量）
参数：expname
A character string, assigning a name to the experiment. This will be used as title in the html output generated by rnaither.
一个字符串，指定名称的实验。这将被用来作为标题在rnaither生成的HTML输出。
参数：excludeCellcounts
a string constant, one of "none", "lowest", "both", "lowestperplate" or "bothperplate". The default is "none". This parameter can be used to exclude wells from the analysis that have very low or very high numbers of cells.
一个字符串常量，"none"，"lowest"，"both"，"lowestperplate"或"bothperplate"。默认"none"。这个参数可以被用来从分析中排除井单元具有非常低或非常高的数字。
"none"No wells will be excluded based on the number of cells they contain.
“无”，无井将被排除它们含有单元数的基础上。
"lowest", "lowestperplate"The wells with the lowest 5 percent of cellcounts will be excluded from further analysis. "lowest" will consider the entire screen at once, and exclude the wells that are overall the lowest 5 percent. "lowestperplate" will consider each plate separately, excluding on each plate the 5 percent of wells having the lowest cellcounts.
“最低”，“lowestperplate”与最低的5％cellcounts井将被排除在进一步分析。 “最低”会考虑整个屏幕一次，并排除井，整体最低的5％。 “lowestperplate”会考虑每个板块，每个板块井5％的最低cellcounts除外。
"both", "bothperplate"The wells with the lowest and highest 5 percent of cellcounts will be excluded from further analysis. Excluding wells with high cell counts may be useful for image based screens, if it is suspected that cells overlap in images, which might cause problems for image processing. "both" will consider the entire screen at once, and exclude the wells that are overall the lowest and highest 5 percent. "bothperplate" will consider each plate separately, excluding on each plate the 5 percent of wells having the lowest and highest cellcounts.
“都”，“bothperplate”最高和最低的5％cellcounts井将被排除在进一步分析。高单元计数不包括井可能是有用的，基于图像的屏幕，如果它被怀疑，单元重叠的图像，这可能会导致图像处理的问题。 “既”会考虑整个屏幕，并排除井，整体最高和最低的5％。 “bothperplate”会考虑每个板块，每个板块井5％的最低和最高cellcounts除外。
参数：logtransform
A logical variable, specifying whether or not the signal intensities should be log-transformed. Default is FALSE.
一个逻辑变量，指定信号强度是否应该记录转化。默认为false。
参数：normalization
A list of strings containing the normalization steps to carry out. The default are is c("lowess","bscore"). The following normalization procedures are available:
包含标准化的字符串列表步骤进行。默认c("lowess","bscore")。以下标准化的程序是：
"lowess"To carry out lowess normalization. This corrects for effects of cell counts on the signal intensities.
“LOWESS”开展LOWESS标准化。这纠正单元计数信号强度的影响。
"liwong"To carry out Li-Wong rank normalization of the signal intensities.
“liwong”，开展李黄的信号强度排名标准化。
"varadjust"To divide each signal intensity value by the variance of the signal intensities on the respective plate.
“varadjust”每个信号强度值除以各自的板块上的信号强度的变化。
"divnorm"To divide each signal intensity value by the median signal intensity of the respective plate.
“divnorm”每个信号强度值除以各自的板块的平均信号强度。
"quantile"To carry out a quantile normalization on the signal intensities.
“分量”要开展对信号强度的1位数标准化。
"bscore"To carry out a bscore normalization on the signal intensities (corrects for spatial effects on a plate.
“bscore开展对信号强度的1 bscore标准化（校正板的空间影响。
"zscore"To carry out a zscore normalization (subtract median of plate, divide by median absolute deviation per plate).
“zscore”贯彻了zscore标准化（减去板的中位数，由每盘的中位数绝对偏差分）。
"negcontrol"To normalize on the negative controls - subtract median of negative controls, divide by MAD of negative controls, per plate.
“negcontrol”标准化阴性对照 - 中位数减去阴性对照，分为阴性对照疯狂，每盘。
"percontrol"To do a percentage of controls normalization - Rescale signal intensities so that mean of negative controls is 100, mean of positive controls is 0.
“percontrol控制标准化的百分比 - 重缩放的信号强度，使阴性对照的平均值为100，平均阳性对照为0。
"percneg"To do a percentage of negative controls normalization - set mean of negative controls to 100, zero signal intensity remains at 0. Normalization routines will be executed in the order as they occur in the list.
“percneg”做阴性对照标准化的百分比 - 阴性对照组平均100，零信号强度保持为0。标准化程序将被执行的顺序，因为他们在名单中出现。
参数：test
Specify what statistical test should be used to identify hits. One of
指定应该使用什么样的统计测试来确定命中。一
"ttest"to carry out a t-test if the mean score for a given siRNA / Gene is 0.
“TTEST”进行了t检验，如果对于一个给定的基因的siRNA /平均得分为0。
"wilcox"to carry out a Wilcoxon test if the mean score for a given siRNA / Gene is 0.
“威尔科克斯”进行了Wilcoxon检验，如果对于一个给定的基因的siRNA /平均得分为0。
"none"to carry out no statistical test.
“无”，开展无统计学测试。
The default is "ttest".
默认是“TTEST”。
参数：scorethresh
The threshold on the normalized score to be used to identify hits. The default is 2.0, hence siRNAs with score > +2 or score < -2 are considered hits.
归得分被用来确定命中的阈值。默认为2.0，因此与得分的siRNAs> +2或得分<-2被视为命中。
参数：pvalthresh
The threshold on the p-value from the statistical test to be used to identify hits. The default is 0.05
从统计检验被用来确定命中p值的阈值。默认是0.05
参数：dogo
A logical variable, specifies whether or not a Gene Ontology-based analysis should be carried out. This parameter is currently ignored, GO is presently not supported nby the rnaither wrapper.
一个逻辑变量，指定是否进行基因本体论为基础的分析应。目前忽略此参数，走的是目前不支持nbyrnaither包装。
参数：outdir
a string specifying the directory in which the results should be stored. Can be an absolute or relative path.
一个字符串，指定结果应存放的目录。可以是绝对或相对路径。
参数：layoutnames
A list of strings, that can be used to assign names to different layouts in the screen. The list should contain the same number of elements as there are different layouts in the screen. These names will be used as labels for the layouts in the html output. If this parameter is not specified, layouts will be numbered in the canonical way.
一个字符串列表，可以用来指定名称在屏幕上不同的布局。该列表应包含相同数量的元素，在屏幕上有不同的布局。这些名字将被用来作为标签在HTML输出的布局。如果这个参数没有被指定，布局将在规范的方式编号。
参数：makeplots
TRUE or FALSE, if set to FALSE, only a subset of the quality control plots will be generated. This speeds up processing, but will result in missing images in the html output.
如果设置为FALSE，TRUE或FALSE，只有一部分的质量控制图将产生。后续处理这个速度，但会导致丢失在HTML输出的图像。
参数：reorder
logical variable, indicating whether dataset should be reordered prior to processing further. This is recommended if the data frame is incomplete, i.e. if wells or plates are missing completely. reorder=T will considerably slow down the analysis.
逻辑变量，表示是否应重新排序前处理进一步集。这是推荐的，如果是不完整的数据框，即如果井或板完全失踪。 reorder=T将大大减缓了分析。
值----------Value----------
Generates the html output file index.html in the directory specified by the outdir parameter.
生成HTML输出文件index.html在outdir参数指定的目录。
举例----------Examples----------
data(exampleDataset, package="RNAither")
rnaither(dataset, expname="Example", excludeCellcounts="none", logtransform=FALSE, normalization=c("lowess","zscore"), test="none", scorethresh=2.0, pvalthresh=0.05, outdir="results")
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 13:16:03
