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

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loadmirnatogene(miRNApath)
loadmirnatogene()所属R语言包：miRNApath

                                        Load miRNA to gene associations for miRNApath
                                         加载的miRNA基因协会对miRNApath

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This method loads associations between miRNAs to the genes they affect.
此方法加载它们影响的基因的miRNA之间的关联。


用法----------Usage----------


loadmirnatogene(mirnafile, mirnaobj, mirnacol="miRNA Name",
genecol="Entrez Gene ID", columns=NA)



参数----------Arguments----------

参数：mirnafile
The tab-delimited miRNA results file to be loaded. The file is expected to be in tall-skinny format.  
加载文件的制表符分隔的miRNA的结果。预计将在高大骨感格式的文件。


参数：mirnaobj
An object of type mirnapath containing data resulting from the loadmirnapath method.  
包含数据从loadmirnapath方法一个类型mirnapath对象。


参数：mirnacol
The name of the column header which contains the miRNA names being assayed. That is, the name of the column header in the file being read.  
列标题的名称，其中包含被检测的miRNA名称。也就是说，在被读取的文件的列标题的名称。


参数：genecol
The name of the column header which contains the gene names being assayed.  
列标题的名称，其中包含被检测的基因名称。


参数：columns
The names of any additional columns in the file being read which should equate with the mirnapath object.  
正在读取文件中的任何其他列的名称应等同与mirnapath对象。


Details

详情----------Details----------

The data is expected to have miRNA names which exactly match those in the mirnaTable item of the mirnapath object. Also, the gene names are expected to match exactly with those gene names loaded by loadmirnapathways.
预计将有miRNA的名称完全匹配那些在的mirnapath对象mirnaTable项目数据。此外，基因名称，预计配合loadmirnapathways加载这些基因的名称完全相同。


值----------Value----------

The method returns an object of type mirnapath, a list with components:
该方法返回一个对象，一个组件的列表类型mirnapath：


参数：mirnaTable
data.frame containing the miRNA results data  
数据框包含miRNA的结果数据


参数：columns
list containing the names of required column headers associated to the actual column header supplied in the dataset contained in mirnaTable. Required headers: mirnacol, assayidcol. Optional headers: groupcol, pvaluecol, foldchangecol, expressioncol, filterflagcol  
包含关联到实际列头在包含在mirnaTable数据集提供所需的列头名的名单。所需头文件：mirnacol，assayidcol。可选的标题：groupcol，pvaluecol，foldchangecol，expressioncol，filterflagcol


参数：groupcount
the number of groups contained in mirnaTable using the groupcol, if supplied  
包含在mirnaTable使用groupcol，如果提供的组数


参数：state
the current state of the object, using the following values in order of progress through the typical workflow: unfiltered, filtered, enriched.  
对象的当前状态，为了进步，通过典型的工作流程使用以下值：未经过滤，过滤，丰富。


作者（S）----------Author(s)----------


James M. Ward <a href="mailto:jmw86069@gmail.com">jmw86069@gmail.com</a>



参考文献----------References----------

in Alzheimer's disease brain and CSF yields putative  biomarkers and insights into disease pathways, Journal of Alzheimer's Disease 14, 27-41.

参见----------See Also----------

loadmirnapath filtermirnapath loadmirnatogene loadmirnapathways
loadmirnapathfiltermirnapathloadmirnatogeneloadmirnapathways


举例----------Examples----------



## Load miRNA expression data from AD miRNA paper[＃从公元miRNA的纸装入miRNA表达数据]
## This data contains miRNA expression data, [＃此数据包含miRNA表达数据，]
data(mirnaobj);

## Display the state, which should generally be "unfiltered"[＃显示状态，一般应是“未经过滤”]
## at this point[＃在这一点上]
mirnaobj@state;

## Display summary information about the object[＃显示对象的摘要信息。]
mirnaobj;

## Annotate hits by filtering by P-value 0.05[＃注解命中过滤的P-值0.05]
mirnaobj <- filtermirnapath( mirnaobj, pvalue = 0.05,
    expression = NA, foldchange = NA );

## Write a file as example of required input[＃写的一个文件所需的输入为例]
write.table(mirnaobj@mirnaGene, file = "mirnaGene.txt",
    quote = FALSE, row.names = FALSE, col.names = TRUE, na = "",
    sep = "\t");

## Load the miRNA to gene associations[＃加载的miRNA基因协会]
mirnaobj <- loadmirnatogene( mirnafile = "mirnaGene.txt",
    mirnaobj = mirnaobj, mirnacol = "miRNA Name",
    genecol = "Entrez Gene ID",
    columns = c(assayidcol = "ASSAYID") );

## Display summary, noting the number of genes reported[＃显示摘要，并指出基因数目报道]
mirnaobj;

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


注：
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