R语言 GGBase包 smlSet-class()函数中文帮助文档(中英文对照)

loveR

smlSet-class(GGBase)
smlSet-class()所属R语言包：GGBase

                                        Documentation on S4 class "smlSet" an eSet-derived container for SnpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray
                                         文件上S4类的“smlSet”ESET SnpMatrix名单派生容器，允许SNP芯片的基因分型芯片的有效结合

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Documentation on S4 class "smlSet" an eSet-derived container for SnpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray
文件上S4类的“smlSet”ESET SnpMatrix名单派生容器，允许SNP芯片的基因分型芯片的有效结合


类的对象----------Objects from the Class----------

Objects can be created by calls of the form new("smlSet", assayData, phenoData, featureData, experimentData, annotation, ...). These objects respond to interrogation on samples, expression values, SNP values, and other metadata.
创建对象可以通过检测的形式new("smlSet", assayData, phenoData, featureData, experimentData, annotation, ...)。这些对象回应审讯样品，表达值，SNP的价值观，和其他元数据的。


插槽----------Slots----------




smlEnv: Object of class "environment" an environment with single key smList pointing to a list of
smlEnv类"environment"环境与单一关键对象smList指向的列表




organism: Object of class "character" informal,
organism：类"character"非正式的对象，




assayData: Object of class "AssayData" intended
assayData：Object类的"AssayData"意




phenoData: Object of class "AnnotatedDataFrame"
phenoData类"AnnotatedDataFrame"：对象




featureData: Object of class "AnnotatedDataFrame"  standard feature-level metadata container, implied usage is for documenting
featureData：Object类的"AnnotatedDataFrame"标准功能级别的元数据的容器，使用暗示的记录




experimentData: Object of class "MIAME" standard
experimentData：Object类的"MIAME"标准




annotation: Object of class "character" vector giving the Bioconductor annotation package
annotation：对象类"character"向量Bioconductor注解包




.__classVersion__: Object of class "Versions" class
.__classVersion__类"Versions"类的对象


延伸----------Extends----------

Class eSet, directly. Class VersionedBiobase,  by class "eSet", distance 2. Class Versioned, by class "eSet",  distance 3.
类eSet，直接。类VersionedBiobase，“ESET”级，距离为2。类Versioned，“ESET”级，距离3。


方法----------Methods----------




smList signature(x = "smlSet"): retrieves the
smListsignature(x = "smlSet")：检索




smlEnv signature(x = "smlSet"): retrieves the
smlEnvsignature(x = "smlSet")：检索




exprs signature(x = "smlSet"): retrieves the
exprssignature(x = "smlSet")：检索




snps signature(x = "smlSet", chr = "chrnum"): retrieves the raw matrix of genotype values (SnpMatrix instance from
单核苷酸多态性signature(x = "smlSet", chr = "chrnum")：检索基因型值的原始矩阵（SnpMatrix实例从




combine: concatenates expression
combine：串联表达




getAlleles(smlSet, rsid): returns A/B notations for SNP
getAlleles(smlSet, rsid)：返回的SNP的A / B的符号




coerce: extracts exprs, phenoData and annotation and
coerce：的提取exprs，phenoData和注释




nsFilter: apply nsFilter
nsFilter：适用于nsFilter




[ signature(x = "smlSet", i = "ANY", j = "ANY", drop = "ANY"): Quick methods for subsetting elements of smlSets have been provided.  
[signature(x = "smlSet", i = "ANY", j = "ANY", drop = "ANY")：已提供用于子集smlSets元素的快速方法。

If X is an smlSet instance and G is a vector of class probeId-class, then X[G,] will reduce the expression data to the probes specified in G.
如果X是一个smlSet实例，G是一类向量probeId-class，X[G,]将减少在G指定的探针的表达数据。

If X is an smlSet instance and G is a vector of class chrnum-class, then X[G,] will reduce the SNP genotype data to the SNPs resident on chromosomes enumerated in G.
如果X是一个smlSet实例，G是一类向量chrnum-class，X[G,]将减少SNP基因型数据，居住在G列举的染色体的SNP。

If X is an smlSet instance and G is a vector of class rsid-class, then X[G,] will reduce the SNP genotype data to the SNPs enumerated in the dbSNP id  in G.
如果X是一个smlSet实例，G是一类rsid-class，则X[G,]将减少dbSNP的IDG中所列举的单核苷酸多态性SNP基因型数据的向量。


注意----------Note----------

We have included a [ method for SnpMatrix instances
我们已[为SnpMatrix实例方法


作者（S）----------Author(s)----------


VJ Carey <stvjc@channing.harvard.edu>



参见----------See Also----------

GGtools package makes extensive use of these classes and methods.
GGtools包使得这些类和方法的广泛使用。


举例----------Examples----------


showClass("smlSet")
data(smlSet.example)
smlSet.example
validObject(smlSet.example)
# workout on expression components[锻炼上表达组件]
dim(exprs(smlSet.example))
fn = featureNames(smlSet.example)[1:10]
fn
ss2 = smlSet.example[ probeId(fn), ] # restrict exprs to set of probes[限制设置探针的exprs]
dim(exprs(ss2))
# workout on SNP components[锻炼上的SNP组件]
smList(smlSet.example)
dim(smList(ss2)[[1]])
ss2[ chrnum(21), ]  # trivial restriction of SNP to a chromosome[染色体的SNP琐碎的限制]
sn = colnames(smList(ss2)[[1]])[1:20]  # get some dbSNP ids[得到一些dbSNP的IDS]
ss3 = ss2[ rsid(sn), ]   # subset the snps[子集的单核苷酸多态性]
dim(smList(ss3)[[1]])
dim(smList(ss3)[["21"]]) # check names[检查名称]
ss3
as(snps(ss3, chrnum(21)), "character")[1:5,1:5] # generic codes[通用码]
as(snps(ss3, chrnum(21)), "numeric")[1:5,1:5]  # number copies of B[份数的B]
as(snps(ss3, chrnum(21)), "matrix")[1:5,1:5]  # raw[原]

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。