R语言 cellHTS2包 getTopTable()函数中文帮助文档(中英文对照)

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getTopTable(cellHTS2)
getTopTable()所属R语言包：cellHTS2

                                        Generate the hit list from a scored cellHTS object
                                         生成从刻痕cellHTS对象的命中列表

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Generate the hit list from a scored cellHTS object and write it to a tab-delimited file.
生成从1刻痕cellHTS对象的暗杀名单，并把它写入制表符分隔的文件。


用法----------Usage----------



getTopTable(cellHTSlist, file="topTable.txt", verbose=interactive())




参数----------Arguments----------

参数：cellHTSlist
a list of cellHTS objects. See details.
cellHTS对象名单。查看详情。


参数：file
the name of the output file. Default is "topTable.txt".
输出文件的名称。默认是“topTable.txt”。


参数：verbose
a logical value, if TRUE, the function reports its progress. Defaults to the state of interactive().
一个逻辑值，如果TRUE，功能报告其进展情况。默认的状态interactive()。


Details

详情----------Details----------

Argument cellHTSlist should be a list containing at least one component named "scored" which corresponds to a scored cellHTS object. Other possible components of cellHTSlist can be:
参数cellHTSlist应该是一个列表，其中包含至少一个组件名为“拿下”，这相当于1拿下cellHTS对象。 cellHTSlist其他可能的组成部分，可以：




"raw":  a cellHTS object containing unpreprocessed
"raw"：cellHTS对象，其中包含unpreprocessed




"normalized": a cellHTS object containing normalized data. I.e. state(cellHTSlist[["normalized"]])["normalized"]=TRUE
"normalized"：cellHTS对象，其中包含规范化的数据。即state(cellHTSlist[["normalized"]])["normalized"]=TRUE

All of the components of cellHTSlist should be cellHTS objects containing data from the same experiment, but in different preprocessing stages.
所有的组件cellHTSlist应该是cellHTS含有相同的实验数据的对象，但在不同的预处理阶段。

This function generates a data.frame that is written to file.  This data.frame and the output file contain the list of scored probes ordered by decreasing score values. They have one row for each well and plate, and contain the following columns (depending on the components of cellHTSlist):
这个函数生成一个写入data.frame的file。这个数据框和输出文件包含降低分值下令砍下探针。他们育有一排，每口井和板包含以下各列（取决于组件的cellHTSlist）：




plate:  plate identifier for each well.
plate：每口井的板标识符。




position:  gives the position of the well in the plate
position：提供良好的位置，在板




well:  gives the alphanumeric identifier for the wells.
well：给井字母标识符。




score:  content of slot assayData of the scored cellHTS object given in
score：槽的内容assayData打进cellHTS对象给予




codewellAnno: ell annotation as given by the plate
codewellAnno：ELL注释板




codefinalWellAnno: gives the final well annotation for the scored values.  It combines the information given in the plate configuration file with the values in assayData slot of the scored cellHTS object, in order to have into account the wells that have been flagged either by the screen log file, or manually by the user during the analysis. These flagged wells appear
codefinalWellAnno：给出最终得分值以及注释。它结合了信息板配置文件与assayData的刻痕槽cellHTS对象，为了考虑到已标记的屏幕log文件的井，或值手动在分析过程中的用户。出现这些标记井




raw_ri_chj:  (if cellHTSlist[["raw"]] is given) contains the raw intensities for replicate i in channel j (content of slot assayData of the cellHTS
raw_ri_chj（cellHTSlist[["raw"]]）包含原始强度复制i渠道j（槽的内容assayDatacellHTS




median_chj:  (if cellHTSlist[["raw"]] is given) corresponds to the median of raw measurements across replicates in
median_chj（cellHTSlist[["raw"]]）对应的原始测量的中位数在复制




diff_chj:  (if cellHTSlist[["raw"]] is given and if there are two replicates or samples) gives the difference between
diff_chj：（cellHTSlist[["raw"]]如果给出，如果有2复制或样品）给人的区别




average_chj:  (if cellHTSlist[["raw"]] is given and if there are more than 2 replicates or samples) corresponds to
average_chj：（如果cellHTSlist[["raw"]]如果有超过2复制或样品），对应




raw/PlateMedian_ri_chj:  (if cellHTSlist[["raw"]] is given) this column gives the ratio between each raw measurement and the median intensity in each plate for replicate (or sample) i in channel j. The plate median is determined for the raw intensities using exclusively the wells annotated as
raw/PlateMedian_ri_chj（cellHTSlist[["raw"]]）列了在每块板之间的比率每个原始测量和中位数强度i渠道j复制（或样品） 。被确定为专门标注为井使用的原料强度板块中位数




normalized_ri_chj:  (if cellHTSlist[["normalized"]] is given) gives the normalized intensities for replicate (sample) i in channel j. This corresponds to the content of slot assayData of the cellHTS object given in
normalized_ri_chj（cellHTSlist[["normalized"]]）提供了复制的规范化强度（样本）的i在通道j。这相当于槽的内容assayDatacellHTS对象

Additionally, if the cellHTS object given in cellHTSlist[["scored"]] is already annotated, the output topTable also contains the gene annotation stored in slot featureData.
此外，如果cellHTS对象cellHTSlist[["scored"]]是已经注明，输出topTable还包含了基因注释存储在插槽featureData。


值----------Value----------

Generates the file with the hit list and outputs a data.frame with the same contents.
命中列表生成的文件，并输出一个具有相同内容的data.frame。


作者（S）----------Author(s)----------


Ligia P. Bras <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>



参考文献----------References----------

screens, Genome Biology 7, R66.

参见----------See Also----------

cellHTS
cellHTS


举例----------Examples----------


    data(KcViabSmall)
    xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
    xsc <- scoreReplicates(xn, sign="-", method="zscore")
    xsc <- summarizeReplicates(xsc, summary="mean")
    out <- getTopTable(cellHTSlist=list("raw"=KcViabSmall, "normalized"=xn, "scored"=xsc), file=tempfile())

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


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