mirnapath-class(miRNApath)
mirnapath-class()所属R语言包：miRNApath
S4 class mirnapath and its "show" method
：S4一流mirnapath和其“作秀”的方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
miRNApath class intended to contain miRNA data, gene and pathway associations, and ultimately the pathway
miRNApath类旨在遏制miRNA的数据，基因和途径协会，并最终途径
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("mirnapath", ...).
创建对象可以通过检测的形式new("mirnapath", ...)。
插槽----------Slots----------
Object of class "data.frame", containing the miRNA results data, expected to contain columns with miRNA name, gene name, and ideally some column(s) for filtering hits versus background, e.g. fold change, expression abundance, P-value. Once the data is filtered (see state below) there will be a column with a flag indicating which entries are hits and which are considered background. This column is found in mirnaobj@columns["filterflagcolumn"] and is typically "FILTERFLAG".
对象类的"data.frame"，含miRNA的结果数据，预计将包含与miRNA的名称，基因名称，和理想的某些列（S）过滤与背景的命中列，例如：倍的变化，表达丰度，P值。一旦数据被过滤（看到下面的状态）会有一个标志，指示项安打，被认为背景列。这列被发现在mirnaobj@columns["filterflagcolumn"]通常是"FILTERFLAG"。
Object of class "character", Named list of column headers used throughout the analysis. The purpose of the names is partly to retain the original headers in the mirnaTable data.frame, and partly to coordinate the names with the miRNA-gene and gene-pathway tables used later in the analysis. The recognized headers: mirnacol, assayidcol, genecol, pvaluecol, foldchangecol, pathwaycol, pathwayidcol, groupcol, mirnagene. See the documentation for the mirnapath object type for more details about usage.
对象的类"character"，命名整个分析过程中使用的列标题的列表。名称的目的是部分原头保留中的mirnaTable的数据框，部分配合使用后，在分析miRNA的基因和基因通路中的表的名称。公认的标题：mirnacol, assayidcol, genecol, pvaluecol, foldchangecol, pathwaycol, pathwayidcol, groupcol, mirnagene。看到有关使用更多细节mirnapath对象类型的文档。
Object of class "numeric", indicating how many sample groups are available in the data, provided for convenience.
Object类的"numeric"，说明是多少样本组提供的数据，提供了方便。
Object of class "character", indicating the current analysis state, with values: "unfiltered" if results are loaded but not yet filtered; "filtered" if results are loaded and hits are defined with the filterflagcol column; "enriched" if the data is loaded, filtered, and analyzed for enrichment. One can load mirna-gene and gene-pathway data at any point which necessitates using the mirnaobj@mirnaGene or mirnaobj@mirnaPathways object elements to determine if that data has been loaded.
类的对象"character"，说明目前的状态分析，与价值观："unfiltered"如果结果被加载，但尚未过滤;"filtered"如果结果加载命中与filterflagcol列定义; "enriched"如果加载数据，过滤，浓缩分析。人们可以在任何时候需要使用mirnaobj@mirnaGene或mirnaobj@mirnaPathways对象元素，以确定是否这些数据已加载加载miRNA的基因和基因通路的数据。
Object of class "data.frame", containing associations between miRNA and genes. The data should contain one miRNA-to-gene relationship per row, and should contain only those two columns. Additional columns are maintained but ignored. Note that one can use any values in the genecol column, provided they match exactly with values found in the mirnaobj@mirnaPathways element (see below.) Therefore, if desired one can use transcript or gene associations, or other integration methods as desired.
类"data.frame"的对象，包含miRNA与基因之间的关联。数据应该包含每行的miRNA基因的关系，并应只包含两列。维持不变，但忽略额外的列。请注意，人们可以使用任何值在genecol列，提供他们完全匹配的mirnaobj@mirnaPathways元素的值（见下文）。因此，如果需要可以使用所需的誊本或基因协会，或其他集成方法。
Object of class "data.frame", containing gene-pathway associations. The data should contain only one gene-to-pathway association per row of data. The data can have pathway ID values, which may facilitate comparisons to pathway databases (and may allow substantial data volume reduction if necessary.) If there is no pathwayidcol column, then one will be created using a numerical assignments of the pathway names. Note that this conversion is not sensitive to pathway sources, so care should be taken to include pathway source in the pathway name if two sources share the same pathway name. The same is true for pathway ID values, should they be purely numerical and have shared values across pathway sources.
类"data.frame"对象，包含基因途径商会。数据应该包含每行数据的基因只有一个途径协会。数据可以有途径ID值，这可能比较方便通路数据库（可能允许大量数据，如果必要的体积减少。）如果有是没有pathwayidcol的列，然后将创建一个数值分配的途径名。请注意，这个转换是不敏感途径来源，以便照顾应采取包括在通路名称通路源，如果有两个来源共用同一通路名称。同样是真实的途径ID值，他们应该是纯粹的数值和共享跨通路来源的值。
Object of class "numeric", Numerical value indicating how many pathways are available in the data, provided for convenience.
Object类的"numeric"，数值是多少途径提供的数据，提供了方便。
Object of class "numeric", List of filters applied to the data, which may include: "P-value", "Fold change", and/or "Expression".
对象类"numeric"，过滤器适用于数据，其中可能包括名单："P-value", "Fold change"和/或"Expression"。
Enrichment summary data in the form of a list of elements for each sample group (the sample group is the name of each element.) Each list element is itself a list with enrichment result data for each sample group, as independently calculated: "pvalues" - list of P-values named by pathway ID; "Measured pathway mirnaGenes" - total number of miRNA-gene-pathway combinations measured, which gives some idea of the overall coverage of pathways. The general point is that miRNAs have the potential to cover many genes and pathways; "Total mirnaGenes" - number of miRNA-gene combinations represented in the data; "Enriched pathway mirnaGenes" - number of miRNA-gene values enriched in the pathway tested; "Enriched by miRNA" - list of miRNAs involved in the pathway tested, with the list of genes in parentheses per miRNA; "Enriched by Gene" - same as previous except switching gene and miRNA; "Total enriched mirnaGenes" - the total number of miRNA-gene values involved in any pathway enrichment (significant or not.) The total values are useful when comparing across sample groups, looking particularly for groups with few changes or those with a uniquely high number of changes.
浓缩在每个样本组（样本组的每个元素的名称）的元素的列表，每个列表元素本身是一个与每个样品组的富集结果数据列表汇总数据，作为独立的计算：<X > - 通路编号命名的P值列表; "pvalues" - miRNA的基因通路组合的总数量来衡量，整体覆盖的途径提供了一些想法。一般点的miRNA有可能涉及许多基因和途径; "Measured pathway mirnaGenes" - "Total mirnaGenes" - 丰富的miRNA基因值在测试通路miRNA的基因组合中的数据代表的数量; ;"Enriched pathway mirnaGenes" - 测试列表的途径参与miRNA的基因在每个miRNA的括号列表，"Enriched by miRNA" - 与以前一样，除了开关基因和miRNA;"Enriched by Gene" - 总数参与任何途径富集（显着与否，）miRNA的基因值，总价值是整个样本组进行比较时，寻找一些变化或独特的高数量的变化，特别是有用的。
Object of class "character", pathways contained in the mirnaobj@mirnaPathways object, named by the pathway ID values found in the pathwayidcol column. This list facilitates converting the data in the enrichment element to pathway names, since those values are named by the pathway ID to conserve memory.
"character"类的对象，途径mirnaobj@mirnaPathways对象名为ID在pathwayidcol列值的途径，包含。这个名单有利于转换的丰富元素的数据通路的名字，因为这些值的途径编号命名，以节省内存。
方法----------Methods----------
show signature(object = "mirnapath"): ...
显示signature(object = "mirnapath")：...
源----------Source----------
Journal of Alzheimers Disease 14, 27-41.
[老年性痴呆14，27-41。
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.
举例----------Examples----------
library(miRNApath);
data(mirnaobj);
# the slotNames and definitions are described[的slotNames和定义描述]
#showClass(mirnaobj);[showClass（mirnaobj）;]
# Default "show" method describes the contents of the object[默认的“秀”的方式介绍对象的内容]
mirnaobj;
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 01:03:06
