vaFilter(VariantAnnotation)
vaFilter()所属R语言包：VariantAnnotation
Functions for VariantAnnotation filters
VariantAnnotation过滤器的功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions create instances of VAFilter objects. Filters can be applied to genomic variants in a GRanges object. The object returned contains a logical vector indicating which records satisfied the filter and stats on how many elements satisfied the filter.
这些功能创建VAFilter对象的实例。过滤器可以应用于基因变种GRanges对象。返回的对象包含一个逻辑向量，说明它记录满足多少元素满足过滤器的过滤器和统计。
用法----------Usage----------
vaFilter(fun, name = NA_character_, ...)
## S4 method for signature 'missing'
vaFilter(fun, name=NA_character_, ...)
## S4 method for signature 'function'
vaFilter(fun, name=NA_character_, ...)
compose(filt, ..., .name)
dbSNPFilter(dbSNP=character(0), .name="dbSNPFilter")
regionFilter(txdb, region="coding", .name="regionFilter")
参数----------Arguments----------
参数：fun
An object of class function to be used as a filter. fun must accept a single named argument x, and is expected to return a logical vector such that x[fun(x)] selects only those elements of x satisfying the conditions of fun
function类的对象被用作过滤器。 必须接受fun单一命名参数x，预计返回一个逻辑向量x[fun(x)]x满足fun的条件只选择那些元素
参数：name
A character(1) object to be used as the name of the filter. The name is useful for debugging and reference.
过滤器的名字被用来作为一个character(1)对象。 name是有用的调试和参考。
参数：filt
A VAFilter object, to be used with additional arguments to create a composite filter.
一个VAFilter对象，将使用额外的参数，创建一个复合过滤器。
参数：.name
An optional character(1) object used to over-ride the name applied to default filters.
一个可选的character(1)对象使用过骑适用于默认过滤器的名称。
参数：dbSNP
The character(0) name of the dbSNP package to be used. The default (character(0)) performs no filtering
character(0) dbSNP的包要使用的名称。默认（character(0)）不执行过滤
参数：txdb
The TranscriptDb object used to identifying gene regions.
TranscriptDb对象用来确定基因区域。
参数：region
A character(1) object specifying the region on which to filter the results. Possible values are "coding", "intron", "3UTR", "5UTR" and "intergenic".
一个character(1)对象指定区域上筛选结果。可能的值是“编码”，“内含子”，“3UTR”，“5UTR的”和“间隔”。
参数：...
Additional arguments
额外的参数
Details
详情----------Details----------
vaFilter allows users to construct their own filters. The fun argument to vaFilter must be a function accepting a single argument x and returning a logical vector indicating which records passed the filter.
vaFilter允许用户建立自己的过滤器。 funvaFilter参数必须是一个函数接受一个参数x和返回的记录通过过滤器的一个逻辑向量。
The signature(fun="missing") method creates a default filter that returns a vector of TRUE values with length equal to length(x).
signature(fun="missing")方法创建一个默认的过滤器，返回TRUE值的向量长度等于length(x)。
compose constructs a new filter from one or more existing filter. The result is a filter that returns a logical vector with indices corresponding to components of x that pass all filters. If not provided, the name of the filter consists of the names of all component filters, each separated by " o ".
compose构造一个新的过滤器由一个或多个现有的过滤器。结果是一个过滤器，对应x通过所有过滤器组件与指数返回一个逻辑向量。如果不提供，过滤器的名称，包括所有组件过滤器，每个" o "分隔的名称。
The remaining functions documented on this page are built-in filters that accept arguments x, subset=TRUE and return a logical vector of length(x) indicating which components of x satisfy the filter.
此页面上剩余的记录功能，内置的过滤器，接受参数x, subset=TRUE返回一个逻辑向量length(x)说明哪些组件x满足过滤器。
dbSNPFilter selects elements present in the specified dbSNP package
dbSNPFilter选择元素存在于指定dbSNP的包
regionFilter selects elements present in the region specified.
regionFilter选择在指定的区域目前的元素。
值----------Value----------
vaFilter returns an object of VAFilter.
vaFilterVAFilter返回一个对象。
Filters return a logical vector of length(x), with TRUE indicating components that pass the filter.
过滤器返回length(x)的逻辑向量，TRUE显示元件，通过过滤器。
作者（S）----------Author(s)----------
Valerie Obenchain <vobencha@fhcrc.org>
参见----------See Also----------
VAFilter
VAFilter
举例----------Examples----------
data(variants)
# variants present in dbSNP [变种呈现在dbSNP数据库]
snpFilt <- dbSNPFilter("SNPlocs.Hsapiens.dbSNP.20090506")
# subset of variants that passed the filter[变种的子集，通过过滤器]
snpFilt(variants)
# VAFilterResult with logical vector indicating which variants passed the filter[VAFilterResult逻辑向量指示变种通过过滤器]
snpFilt(variants, subset=FALSE)
# variants present in coding regions [变异存在于编码区]
library(TxDb.Hsapiens.UCSC.hg18.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene
regionFilt <- regionFilter(txdb, region="coding")
regionFilt(variants, subset=FALSE)
# subset of variants that passed both filters[变种的子集，通过两个过滤器]
comboFilt <- compose(snpFilt, regionFilt)
comboFilt(variants)
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。
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发表于 2012-2-26 15:57:56
