ENVISIONQuery(ENVISIONQuery)
ENVISIONQuery()所属R语言包：ENVISIONQuery
Launch a query against Envision, a web online query system...
推出针对预想的查询，网上在线查询系统...
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Launch a query against Envision, a web online query system providing elaborated information for EnCORE services.
启动反对预想的查询，网络在线查询系统阐述ENCORE服务信息。
用法----------Usage----------
serviceName="menu", toolName="menu", chunk=1000, details=TRUE,
writeHTML=FALSE, testMe=FALSE,
graphicMenu=getOption("menu.graphics"), formatIt=TRUE,
参数----------Arguments----------
参数：ids
Depending on input type, IDs for desired objects as a character vector a character string containing the entire Enfin xml document or a name of an Enfin xml file.
根据输入类型，字符串包含整个Enfin XML文件或一个Enfin XML文件的名称作为一个特征向量所需的对象的ID。
参数：typeName
Type of input ids. If 'menu' (default), a menu is constructed allowing to choose one of the available types.
输入IDS类型。如果菜单（默认），构造一个菜单，可以选择可用的类型之一。
参数：serviceName
The Envision service name or a character vector of service names. In a latter case system compbines requests into pipeline using the output of current service request as an input for a next one. If 'menu' (default), the menu is contructed allowing to choose one of the available services.
该设想的服务名称或服务名称的字符向量。在后一种情况下系统compbines管道，将使用当前服务请求的输出作为输入的下一个请求。如果菜单（默认），菜单线外，允许选择一个可用的服务。
参数：toolName
The tool for a particular envision service. If 'menu' (default) and there is more than one tool available, a menu is contructed allowing to choose one of the available tools.
对于一个特定的工具设想服务。如果菜单（默认），并有超过一个工具可用，会应用菜单，可以选择可用的工具之一。
参数：chunk
The number of IDs retrieved during a single query session. In case the number of IDs exceeds the chunk size, the whole ID set is retrieved during multiple query sessions overcoming the potential limitations on a single query session ID set size. If NA, a single session is used. Default is 1000.
在一个单一的查询会话的ID号码检索。在情况的ID数量超过块大小，整个标识集克服潜在限制在一个单一的查询会话ID集大小的会议期间多个查询检索。如果不适用，使用一个会话。默认值是1000。
参数：details
If TRUE (default), a list of intermediate results is returned; otherwise, just the final query result. Note: not implemented at this time
如果为TRUE（默认），中间结果的列表，则返回，否则，只是最终的查询结果。注：此时不实施
参数：writeHTML
If TRUE (default is FALSE), write the received intermediate HTML to files.
如果为TRUE（默认为false），写中间的HTML文件。
参数：testMe
If TRUE (default is FALSE), assign default values and run.
如果为TRUE（默认为false），指定默认值，并运行。
参数：graphicMenu
If TRUE (default is FALSE), use a GUI window for the pick menus.
如果为TRUE（默认为false），挑菜单使用一个GUI窗口。
参数：formatIt
If TRUE (default), try to interpret the returned character table and structure the result. If false, the character string representing the entire enfinXML file returned by ENVISION. Note: formatting is implemented only for 'Probe2Uniprot' and 'ID conversion' services at this time. If false, the character string representing the entire enfinXML file returned by ENVISION.
如果为TRUE（默认），试图解释返回的字符表和结构的结果。如果为假，返回字符串代表整个enfinXML文件由设想。注意：格式化只有在这个时候实施“Probe2Uniprot”和“ID转换服务。如果为假，返回字符串代表整个enfinXML文件由设想。
参数：options
The (optional)list each element of which represents the <name,value> pair used to apply the additional constraints when sending a query to a particular service (maximum number of pathways for Reactome service as an example)
其中每个元素的代表的<name,value>的一双用来申请额外的限制时将查询发送到一个特定的服务（最高的途径为例数为Reactome服务（可选）名单）
参数：filter
The (optional)list where the name of each element represents the formatted output data frame column on which filetering is to be performed ('organism.species', 'Microarray.platform' etc.) and the list element containing a character vector defining the set of values on which the merging (intersection) for a given column will be performed ('Homo sapiens' for 'organism.species', 'affy_hg_u133_plus_2' for 'Microarray.platform' etc.). The filtering is performed if the list is not empty and the formatIt=TRUE. Default is an empty list.
（可选的）列表，其中每个元素的名称代表格式化输出数据框列filetering上的要执行（organism.species“，”Microarray.platform“等）和列表元素包含一个字符向量定义设定值合并为一个给定列（路口）将执行（organism.species“智人”，affy_hg_u133_plus_2“Microarray.platform”等）。如果列表是空和的formatIt = TRUE，执行筛选。默认是一个空列表。
参数：compact
If TRUE and the formatted output (formatIt = TRUE)is represented by a data frame, collapses the rows with duplicated match sets but different attributes into a single row with unique match set and an attribute list separated by comma for each attribute column. Default is TRUE.
如果是TRUE和格式化输出（formatIt = TRUE），代表一个数据框，倍数成一个独特的比赛设置和属性列表，以逗号分隔每个属性列单列行与复制的比赛，但是不同的属性。默认值是TRUE。
参数：verbose
If TRUE (default is FALSE), more debugging information is printed. </table>
如果为TRUE（默认为false），更多的调试信息被打印出来。 </ TABLE>
值----------Value----------
The ENVISIONQueryResult structure or NULL if no results were found.
ENVISIONQueryResult结构或NULL，如果没有结果发现。
注意----------Note----------
For a pipeline of services, only unformatted output supported at this time.
对于服务的管道，此时只有格式化输出支持。
作者（S）----------Author(s)----------
Alex Lisovich, Roger Day
举例----------Examples----------
#convert the Affy probeset IDs to UniProt IDs[UniProt ID的转换的Affy probeset的标识]
res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),
serviceName="ID Conversion",toolName="Affy2Uniprot",typeName="Affymetrix ID");
print(res);
#retrieve the pathways for given Uniprot ID(s)[检索的途径，对于给定的Uniprot ID（S）]
res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",typeName="Uniprot ID");
print(res[,-3]);
#retrieve protein-protein interactions[检索蛋白质相互作用]
res<-ENVISIONQuery(ids="P38398",serviceName="Intact",typeName="Uniprot ID");
print(res[1:5,]);
#convert EnSembl IDs to Uniprot IDs[转换ENSEMBL标识Uniprot标识]
res<-ENVISIONQuery(ids=c("ENSP00000397145","ENSP00000269554"),serviceName="Picr",typeName="Protein ID");
print(res);
#### ENVISIONQuery request using options and filters[＃＃ENVISIONQuery的要求使用选项和过滤器]
#match Uniprot IDs to EnSembl and TrEMBL[Uniprot的ID匹配到ENSEMBL和TrEMBL]
options<-list("enfin-picr-search-database"=c("ENSEMBL_HUMAN","TREMBL"));
res<-ENVISIONQuery(ids="P38398",serviceName="Picr",options=options,typeName="Protein ID");
print(res);
#retrieve the pathways for given Uniprot ID(s)sorting them by coverage[由覆盖排序检索途径给予Uniprot编号（S）]
#and calcultating the total protein count[和calcultating总蛋白数]
options<-list("enfin-reactome-add-coverage"="true",
"enfin-reactome-sort-by-coverage"="true");
res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",options=options,typeName="Uniprot ID");
print(res[,-3]);
#convert the Affy probeset IDs to UniProt IDs restricting [转换的Affy probeset的标识UniProt ID的限制]
#output by micro array type and organism species[微阵列类型和生物物种的输出]
filter<-list(Microarray.Platform="affy_hg_u133_plus_2",
organism.species="Homo sapiens");
res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),filter=filter,
serviceName="ID Conversion",toolName="Affy2Uniprot",typeName="Affymetrix ID");
print(res);
#### pipeline of ENVISIONQuery requests. As of recent version, [＃＃＃管道ENVISIONQuery请求。作为最新版本，]
#### output formatting for a pipelined request is not supported yet.[流水线请求＃＃＃输出格式不支持。]
#Intact-Reactome cascaded request for UniProt ID(s). [完整的Reactome级联UniProt ID（S）的请求。]
IntactReactomeXML<-ENVISIONQuery(ids="P38398",
serviceName=c("Intact","Reactome"),typeName="Uniprot ID",verbose=TRUE);
#convert xml text into XMLDocument[转换成XML文本的XMLDocument]
#using XML package for further exploring[为进一步探索利用XML包]
if(!is.null(IntactReactomeXML)){
xmlDoc<-xmlTreeParse(IntactReactomeXML,useInternalNodes = TRUE, asText=TRUE);
class(xmlDoc);
}
#### interactive ENVISIONQuery requests[＃＃＃的互动ENVISIONQuery请求]
## Not run: [＃无法运行：]
res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),filter=filter,
serviceName="menu",toolName="menu",typeName="menu");
print(res);
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。
|
发表于 2012-2-25 17:15:52
