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

loveR

MEDMEset-class(MEDME)
MEDMEset-class()所属R语言包：MEDME

                                        Class "MEDMEset"
                                         类“MEDMEset”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is used in MEDME library to store MeDIP derived DNA-methylation estimates and to save further elaboration of these, in association with chromosomal and positional probe information
这个类是用来存储MeDIP衍生的DNA甲基化的估计，并进一步阐述这些协会与染色体和位置探测信息保存MEDME库，


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

Objects can be created by calls of the form new("MEDMEset", ...). This object could initially host the MeDIP normalized logRatio data, as returned by the MEDME.readFiles function. Afterwards, the same obejct is returned by most of the MEDME library function. Each time, a new slot is filled with additional data, as smoothed logR or Absolute/Relative Methylation Scores (AMS and RMS respectively). At the end of the analysis, usually after a call to the predict function, the MEDME.writeFiles function can be used to generate SGR or GFF files from this object.
创建对象可以通过检测的形式new("MEDMEset", ...)。这个对象最初举办MeDIP归数比数据，MEDME.readFiles函数返回。之后，同样的obejct由大部分的MEDME库函数返回。每次，一个新的插槽填补额外的数据，平滑logR或绝对/相对的甲基成绩（分别为AMS和RMS）。在分析结束后，通常predict函数的调用，MEDME.writeFiles函数可以用于生成可从该对象的SGR的或GFF文件。


插槽----------Slots----------




chr: Object of class "character" : the probe-level chromosome asignments
chr：Object类的"character"：的探针级染色体asignments




pos: Object of class "numeric" : the probe-level genomic position
pos：Object类的"numeric"：基因组探针的位置




logR: Object of class "matrix" : the probe-level un-trasformed normalized MeDIP logRatios for each sample
logR：Object类的"matrix"：探针一级未-trasformed的的每个样品归MeDIP对数比




smoothed: Object of class "matrix" : the probe-level smoothed MeDIP logRatios for each sample
smoothed类"matrix"：探针级平滑每个样品MeDIP对数比对象




AMS: Object of class "matrix"  : the probe-level Absolute Methylation Score for each sample
AMS类"matrix"对象：探针水平绝对甲基分数为每个样品




RMS: Object of class "matrix"  : the probe-level Relative Methylation Score for each sample
RMS类"matrix"对象：探针水平相对甲基分数为每个样品




CGcounts: Object of class "numeric"  : the probe-level count of CpGs
CGcounts：Object类的"numeric"：探针水平计数的CPGs




organism: Object of class "character" : the organism that the probe genomic positions are referring to, either hsa or mmu for homo sapiens or mus musculus respectively
organism：Object类的"character"：生物体探针基因组的位置是指，无论HSA或MMU为智人或小家鼠分别


方法----------Methods----------




[ signature(x = "MEDMEset"): subsets the object based on its probes and/or samples
[signature(x = "MEDMEset")：子集探针和/或样品为基础的对象




AMS signature(object = "MEDMEset"): extracts the Absolute Methylation Score from the AMS slot
医疗辅助队signature(object = "MEDMEset")：提取从AMS插槽绝对甲基分数




CG signature(object = "MEDMEset"): extracts the probe CpG count from the CGcounts slot
企业管治signature(object = "MEDMEset")：提取从CGcounts插槽探针的CpG计数




chr signature(object = "MEDMEset"): extracts the probe chromosomal assignment
CHRsignature(object = "MEDMEset")：提取探针染色体分配




org signature(object = "MEDMEset"): extracts the organism
ORGsignature(object = "MEDMEset")：提取生物




initialize signature(.Object = "MEDMEset"): automatically generates smoothed, AMS and RMS matrix when only the logR slot is filled
初始化signature(.Object = "MEDMEset")：自动生成平滑，AMS和RMS矩阵时只有logR插槽充满




logR signature(object = "MEDMEset"): extracts the matrix of MeDIP un-transformed logRatios
logRsignature(object = "MEDMEset")：提取MeDIP未转化的对数比矩阵




pos signature(object = "MEDMEset"): extracts the probe genomic position
POSsignature(object = "MEDMEset")：提取探针基因的位置




RMS signature(object = "MEDMEset"): extracts the Relative Methylation Score from the RMS slot
RMSsignature(object = "MEDMEset")：从RMS插槽中提取相对甲基分数




show signature(object = "MEDMEset"): prints a summary of the object content
显示signature(object = "MEDMEset")：打印对象的内容摘要




smoothed signature(object = "MEDMEset"): extracts the Absolute Methylation Score from the AMS slot
平滑signature(object = "MEDMEset")：从AMS插槽中提取的绝对甲基分数


作者（S）----------Author(s)----------


Mattia Pelizzola



参考文献----------References----------

<h3>See Also</h3>   <code>MEDME.readFiles</code>, <code>MEDME.writeFiles</code>

举例----------Examples----------


showClass("MEDMEset")

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。