RmiR(RmiR)
RmiR()所属R语言包：RmiR
Coupling miRNA and Gene expression results
耦合miRNA和基因表达的结果
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Coupling miRNA and Gene expression results for a selected target database.
耦合miRNA和基因表达的结果，选定目标数据库。
用法----------Usage----------
RmiR(mirna=NULL,genes=NULL,annotation=NULL,dbname="targetscan",org="Hs",id="probes",id.out="symbol",verbose=FALSE)
read.mir(mirna=NULL,genes=NULL,annotation=NULL,id="probes",dbname=c("targetscan","pictar"),org="Hs",at.least=2,id.out="symbol",verbose=FALSE)
参数----------Arguments----------
参数：mirna
A data.frame with two columns, the first with the microRNA names, the second with the expression values.
一个两列的microRNA名称的第一个第二，表达值数据框。
参数：genes
A data.frame with two columns, the first with gene ID (probes, symbols, ensembl, entrez...), the second with the expression values.
一个有两列，与基因ID（探针，符号，ENSEMBL，Entrez的...）第一第二，表达值数据框。
参数：annotation
The annotation package to annotate the genes file with entrez gene ID, eg: Agilent 44k annotation="hgug4112a.db" or annotation="org.Hs.eg.db" for human not using microarrays probes.
注释包注释基因与Entrez基因身份证，如文件：安捷伦44K注释=“hgug4112a.db”或批注“org.Hs.eg.db”人类不使用芯片探针。
参数：dbname
A selected database of miRNA target. See RmiR.hsa_dbconn, default is "targetscan". If using read.mir it can be a vector of databases, default are "targetscan" and "pictar".
选定数据库的miRNA靶。看到RmiR.hsa_dbconn，默认是“targetscan”。如果使用read.mir它可以是一个数据库的向量，默认的“targetscan”和“PicTar的”。
参数：id
The type of annotation of the genes input file. An accepted value is one of: "genes" for entrez gene id, "probes" for microarray probes id, "ensembl" for ensembl gene id, "unigene" for unigene gene id and "alias" for official gene symbols and aliases.
注释的基因输入文件类型。一个可接受的值是：“基因”Entrez基因ID，ID芯片探针的“探针”，“ENSEMBL”，为ENSEMBL基因身份证“，UniGene的基因ID和”别名“官方基因的UniGene”符号和别名。
参数：id.out
The annotation of the genes in the output. The default it is "symbol", to have the HGNC symbols, it can be also "probes" if the input id is "probes" or "gene" to leave just the entrez gene annotation.
在输出的基因注释。默认是“象征”，，有HGNC符号，它可以是也“探针”，如果输入id是“探针”或“基因”离开只是Entrez基因注释。
参数：at.least
Minimum number of databases that should yeld the result, when the search is performed in multiple databases with read.mir. If it is 1 it is basically an union between databases. Default is 2.
最低数量数据库应该yeld结果，在多个数据库中进行搜索时，与read.mir。如果是1，它基本上是一个数据库之间的联盟。默认值是2。
参数：org
Define the targets database package of the desired organism. Default is "Hs"
定义目标数据库包所需的生物体。默认是“HS”
参数：verbose
If it is desired or not to have some verbose output while analysing the data. Default is FALSE
如果想要或不有一些详细的输出，同时分析数据。默认为false
Details
详情----------Details----------
RmiR couples the gene expression and microRNA expression. It uses the AnnotationDbi package to annotate the gene expression file. We intend to put already filtered and significant values in the input file, so in case of duplicate probes or different sequences identifying the same gene or more than one values for a miRNA, the function will take just the mean of the different results and give the corresponding coefficent of variation. Each input file must have two columns. The first one for annotation, the second for expression value. The name of the columns does not matter.
RmiR夫妇的基因表达的microRNA表达。它使用AnnotationDbi的包注释基因表达的文件。我们打算把输入文件中已经过滤和重大价值，所以在识别相同的基因或多个值的miRNA重复探针或不同序列的情况下，该功能将采取不同的结果只是平均，并给予相应的变异系数。每个输入文件必须有两列。为注释的第一个，第二个表达式的值。列的名称并不重要。
read.mir uses RmiR but performs the search in one or more databases and returns only the object present in at.least databases. If at.least is equal to 1 we basically do an union between the results from the databases of choice, if we specify just a database in dbname it is exactly the same of the RmiR function.
read.mir使用RmiR但在一个或多个数据库，并只返回at.least数据库对象目前执行的搜索。如果at.least是等于1，我们基本上是做一个从数据库选择的结果之间的联盟，如果我们指定是dbname功能完全一样只是在RmiR数据库。
值----------Value----------
参数：mature_miRNA
The resulting miRNAs present in the input file with at least one target in the selected database.
由此产生的miRNA呈现在输入文件至少有一个选定的数据库中的目标。
参数：gene_id
The resulting entrez gene ids present in the input file that are also targets in the selected database.
Entrez基因产生的ID在输入文件，也选定数据库中的目标。
参数：mirExpr
microRNA expression value
microRNA表达价值
参数：geneExpr
Gene expression Value
基因表达的价值
参数：mirCV
miRNA expression coefficent of variation in case of duplication otherwise is NA
在重复的情况下变化的miRNA表达系数，否则是不适用
参数：geneCV
Gene expression coefficent of variation in case of duplication otherwise is NA
在重复的情况下的变异基因的表达系数，否则是不适用
参数：symbol
If the id.out is "symbol".
如果id.out“符号”。
参数：probe_id
If the id.out is "probes".
如果id.out是“探针”。
参见----------See Also----------
RmiR.hsa_dbconn,
RmiR.hsa_dbconn
举例----------Examples----------
## Merge gene expression and mirna expression for agilent IDs[＃合并安捷伦标识基因表达的miRNA表达]
genes <- data.frame(genes=c("A_23_P171258", "A_23_P150053", "A_23_P150053",
"A_23_P150053", "A_23_P202435", "A_24_P90097",
"A_23_P127948"))
genes$expr <- c(1.21, -1.50, -1.34, -1.45, -2.41, -2.32, -3.03)
mirna <- data.frame(mirna=c("hsa-miR-148b", "hsa-miR-27b", "hsa-miR-25",
"hsa-miR-181a", "hsa-miR-27a", "hsa-miR-7",
"hsa-miR-32", "hsa-miR-32", "hsa-miR-7"))
mirna$expr <- c(1.23, 3.52, -2.42, 5.2, 2.2, -1.42, -1.23, -1.20, -1.37)
RmiR(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes")
## Search in pictar[＃在PicTar的搜索]
RmiR(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
dbname="pictar")
## or[＃或]
read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
dbname="pictar", at.least=1)
## Search in miranda, pictar and targetscan, present in each database:[＃米兰达，PicTar的和TargetScan，目前在每个数据库中搜索：]
read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
dbname=c("miranda", "pictar", "targetscan"), at.least=3)
## Search in miranda, pictar and targetscan, present in at least 2 database:[＃米兰达，PicTar的和TargetScan，目前至少有2个数据库中搜索：]
read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id="probes",
dbname=c("miranda", "pictar", "targetscan"), at.least=2)
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 13:04:42
