ExonArray-class(GenomeGraphs)
ExonArray-class()所属R语言包：GenomeGraphs
Class "ExonArray" representing probe level exon array data from Affymetrix
类“ExonArray”代表从Affymetrix的探针水平外显子阵列数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Represents probe level exon array data from Affymetrix. Makes it possible to visualize alternative splicing as measured by the Affymetrix exon array platform and relate it to known transcript isoforms annotated by Ensembl
表示从Affymetrix的探针水平外显子阵列数据。使它可以可视化剪接由Affymetrix的外显子阵列平台测量，并与已知的转录亚型Ensembl的注解
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("ExonArray", ...).
创建对象可以通过检测的形式new("ExonArray", ...)。
插槽----------Slots----------
intensity: Object of class "matrix", array data
intensity：Object类的"matrix"，阵列中的数据
probeStart: Object of class "numeric" vector with the start positions of the probes
probeStart类"numeric"矢量对象的起始位置的探针
probeEnd: Object of class "numeric" vector with the end positions of the probes
probeEnd类"numeric"矢量对象与结束位置的探针
probeId: Object of class "character" vector containing the probeset identifiers
probeId：类对象"character"向量probeset标识符
nProbes: Object of class "numeric" vector defining how many probes there are for each exon/probeset
nProbes：对象类"numeric"向量定义为每个外显子/ probeset有多少探针
displayProbesets: Object of class "logical" used to indicate if probe set names should be plotted or not
displayProbesets：对象类"logical"用来表示如果探针集名称应绘制或不
延伸----------Extends----------
Class "gdObject", directly.
类"gdObject"，直接。
方法----------Methods----------
show signature(object = "ExonArray"): ...
显示signature(object = "ExonArray")：...
作者（S）----------Author(s)----------
Steffen Durinck
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
if(interactive()){
data("unrData", package="GenomeGraphs")
library(biomaRt)
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
title = new("Title", title ="ENSG00000009307", dp = DisplayPars(color = "darkslategray"))
exmapcol = rep("khaki", length(unrNProbes))
exmapcol[28]="darkred"
probeSetCol = rep("grey", length(unrNProbes))
probeSetCol[27:28]="darkslategray"
probeSetLwd = rep(1, length(unrNProbes))
probeSetLwd[27:28]=3
exon = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd), displayProbesets=FALSE)
exon2 = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd, plotMap=FALSE), displayProbesets=TRUE)
affyModel = new("GeneModel", exonStart = unrPositions[,3], exonEnd = unrPositions[,4])
gene = new("Gene", id = "ENSG00000009307", biomart = mart)
transcript = new("Transcript", id ="ENSG00000009307" , biomart = mart)
legend = new("Legend", legend = c("affyModel","gene"), dp = DisplayPars(color= c("darkgreen","orange")))
gdPlot(list(title,exonarray1 = exon2,exonarray2= exon, AffymetrixModel= affyModel, gene, transcript, legend), minBase = min(exon@probeStart), maxBase=max(exon@probeEnd))
}
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 2012-2-25 19:12:37
