features2Probes(Ringo)
features2Probes()所属R语言包：Ringo
Function for mapping genomic features to probes
功能基因组功能映射到探测器
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function creates a mapping between annotated genomic features and probes on the array whose matching genomic positions are stored in a probeAnno environment.
这个函数创建一个注释基因的功能和探测器阵列的基因位置匹配存储在probeAnno环境之间的映射。
用法----------Usage----------
features2Probes(gff, probeAnno, upstream = 5000, checkUnique = TRUE, uniqueCodes = c(0), mem.limit=1e8, verbose = TRUE)
参数----------Arguments----------
参数：gff
data.frame holding genomic feature annotation
data.frame保持基因组功能注释
参数：probeAnno
Object of class environment holding the genomic positions of probes in the ExpressionSet
类的对象environment在ExpressionSet的探针基因的位置
参数：upstream
up to how many bases upstream of annotated genomic features should probes be counted as related to that feature (see details)
到许多碱基上游注释基因的功能应该探针计算有关该功能（见详情）
参数：checkUnique
logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
逻辑;指示是否应使用的探针匹配从probeAnno环境的独特性指标。
参数：uniqueCodes
numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
数字;染色体方面的比赛唯一的probeAnno环境的元素的数字代码表示独特性？
参数：mem.limit
integer value; what is the maximal allowed size of matrices during the computation; see regionOverlap
整型值;什么是允许的最大规模的矩阵在计算过程中，看到regionOverlap
参数：verbose
logical; detailed progress output to STDOUT?
逻辑;详细的进度输出到STDOUT？
值----------Value----------
The results is a list of length equal to the number of rows in the provided gff, the data.frame of genomic features. The names of the list are the names specified in the gff. Each element of the list is specified by the probes mapping into the genomic region from upstream bases upstream of the feature's start site to the feature's end site. The entries itself are either NULL, if no probe was mapped into this region, or a named numeric vector, with its values being the distances of the probes' middle positions to the feature's start site (which depends on the strand the feature is on) and its names being the identifiers of these probes.
结果是一个长度等于行的数量在所提供的gff列表，基因组功能的数据框。 names列表是在gff指定的名称。指定列表中的每个元素映射到基因组区域从探针upstream碱基功能的起始位点上游功能的网站。参赛作品本身不是NULL，如果没有探针被映射到这个区域，或一个名为数值向量，它的价值与功能的起始站点是探针的中间位置的距离（取决于链上的功能）和它的名字，这些探针的标识符。
注意----------Note----------
This resulting mapping is not used excessively by other Ringo functions, so creating this mapping is optional at this time, but it may simplify subsequent gene/transcript-based analyses.
此映射不使用过度由其他林檎功能，所以创建这个映射是可选的，在这个时候，但它可以简化后续的基因/谈话为基础的分析。
Here, the term feature describes a genomic entity such as a gene, transcript, non-coding RNA or a similar feature annotated to a genome. It does NOT refer to oligo-nucleotide or cDNA probes on the microarray.
在这里，术语功能介绍，如基因，成绩单，非编码RNA或类似的功能基因组注释的基因组实体。它不是指的芯片上的寡核苷酸或cDNA探针。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
regionOverlap
regionOverlap
举例----------Examples----------
ringoExampleDir <- system.file("exData",package="Ringo")
load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
trans2Probe <- features2Probes(exGFF, exProbeAnno)
trans2Probe[exGFF$name[match("NUDT2", exGFF$symbol)]]
exGFF[match(names(trans2Probe)[listLen(trans2Probe)>0],exGFF$name),]
trans2Probe[listLen(trans2Probe)==1]
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 12:57:35
