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

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MEDIPSset-class(MEDIPS)
MEDIPSset-class()所属R语言包：MEDIPS

                                        Class "MEDIPSset"
                                         类“MEDIPSset”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is used in the MEDIPS library to store and extract all the MEDIPS objects and inormations generated during the workflow
这个类是用来存储和提取所有的MEDIPS，对象和工作流的过程中产生的inormations在MEDIPS库


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

Objects can be created by calls of the form new("MEDIPSset", ...). Objects of the class contain the information about the provided regions, their chromosome, start, stop and strand informations,  the raw and normalized signals, the sequence pattern positions and informations about all specified parameters. The MEDIPS SET will be created by reading the input regions file using the MEDIPS.readAlignedSequences function and all further slots will be filled during the workflow.
创建对象可以通过检测的形式new("MEDIPSset", ...)。类的对象包含所提供的区域，他们的染色体，启动，停止和钢绞线信息，原材料和规范化的信号，序列模式的位置和指定的参数有关的所有信息有关的信息。将创建的MEDIPS集读取输入区域提交使用功能MEDIPS.readAlignedSequences和所有进一步的插槽将在充满了工作流程。


插槽----------Slots----------




regions_chr: Object of class "character" : the chromosomes of the regions
regions_chr：Object类的"character"：染色体区域




regions_start: Object of class "numeric" : the start positions of the regions
regions_start：Object类的"numeric"：起始位置的区域




regions_stop: Object of class "numeric" : the stop positions of the regions
regions_stop：Object类的"numeric"：停止位置的区域




regions_strand: Object of class "character" : the strand informations of the regions
regions_strand类"character"对象：链信息的区域




number_regions: Object of class "numeric" : the total number of included regions
number_regions："numeric" Object类：包括总人数的区域




pattern_chr: Object of class "character" : the chromosomes of the sequence pattern
pattern_chr：Object类的"character"：染色体的序列模式




pattern_pos: Object of class "numeric" : the positions of the sequence pattern
pattern_pos："numeric"类的对象：序列模式的立场




number_pattern: Object of class "numeric" : the total number of sequence pattern
number_pattern：Object类的"numeric"：序列总数的格局




genome_chr: Object of class "character" : the chromosome of the genomic bins
genome_chr：Object类的"character"：对染色体的基因组箱




genome_pos: Object of class "numeric" : the positions of the genomic bins
genome_pos：Object类的"numeric"：职位基因箱




genome_CF: Object of class "numeric" : the coupling factor at the genomic bins
genome_CF：对象类"numeric"：在基因组箱的耦合系数




genome_raw: Object of class "numeric" : the raw MeDIP-Seq signals at the genomic bins
genome_raw：对象类"numeric"：原料MeDIP-的SEQ信号在基因箱




genome_norm: Object of class "numeric" : the rms values at the genomic bins
genome_norm：Object类的"numeric"：有效值在基因组箱




genome_name: Object of class "character" : the refernce genome
genome_name：Object类的"character"：refernce基因组




bin_size: Object of class "numeric" : the bin size for the genome vector
bin_size：对象类的基因向量的bin "numeric"：大小




extend: Object of class "numeric" : the number of bases by which the regions are extended
extend：Object类的"numeric"：碱基区域扩展




fragmentLength: Object of class "numeric" : the estimated fragment length of the DNA fragments
fragmentLength：Object类的"numeric"：预计片段长度的DNA片段




sample_name: Object of class "character" : the name of the input file
sample_name：对象类"character"：输入文件名




chr_lengths: Object of class "numeric" : the lengths of the chromosomes included within the MEDIPS SET
chr_lengths：Object类的"numeric"：在MEDIPS包括染色体的长度设置




chr_names: Object of class "character" : the names of the chromosomes included within the MEDIPS SET
chr_names：Object类的"character"：内染色体的名字列入MEDIPS设置




seq_pattern: Object of class "character" : the sequence pattern (e.g. CpG)
seq_pattern：对象类"character"：序列模式（如中央人民政府）




distFunction: Object of class "character" : the distance function specified for calculating the coupling factors
distFunction：对象类"character"：指定用于计算耦合因素的距离函数




distFile: Object of class "character" : the file containing the custom distance weights, if provided
distFile：Object类的"character"：该文件包含自定义的距离权重，如果提供




calcurve_mean_signals: Object of class "numeric" : the mean signals of the calibration curve
calcurve_mean_signals："numeric"类的对象：校准曲线的平均信号




calcurve_mean_coupling: Object of class "numeric" : the mean coupling factors of the calibration curve
calcurve_mean_coupling：对象类"numeric"：平均耦合因素的校正曲线




calcurve_var: Object of class "numeric" : the signal variance of the levels of the calibration curve
calcurve_var：对象类"numeric"：信号校准曲线的水平差异




intercept: Object of class "numeric" : the intercept value calculated from the calibration curve
intercept：对象类"numeric"：从校准曲线的截距值计算




slope: Object of class "numeric" : the slope value calculated from the calibration curve
slope：对象类"numeric"：从校准曲线斜率值计算




cali_chr: Object of class "character" : the chromosomes used for calibration
cali_chr：Object类的"character"：染色体用于校准


方法----------Methods----------




bin_size signature(object = "MEDIPSset"): extracts the bins size from the bin_size slot
bin_sizesignature(object = "MEDIPSset")：提取从bin_size插槽箱大小




calcurve_mean_coupling signature(object = "MEDIPSset"): extracts the mean coupling factors of the calibration curve
calcurve_mean_coupling signature(object = "MEDIPSset")：提取校准曲线的平均耦合因素




calcurve_mean_signals signature(object = "MEDIPSset"): extracts the mean signals of the calibration curve
calcurve_mean_signalssignature(object = "MEDIPSset")：校准曲线中提取的平均信号




calcurve_var signature(object = "MEDIPSset"): extracts the variances of the calibration curve
calcurve_varsignature(object = "MEDIPSset")：提取校准曲线的差异




cali_chr signature(object = "MEDIPSset"): extracts the chromosome used for calculating the calibration curve
cali_chrsignature(object = "MEDIPSset")：提取用于计算校准曲线的染色体




chr_lengths signature(object = "MEDIPSset"): extracts the length of the chromosomes included within the MEDIPS SET
chr_lengthssignature(object = "MEDIPSset")：提取染色体内MEDIPS集的长度




chr_names signature(object = "MEDIPSset"): extracts the names of the chromosomes included within the MEDIPS SET
chr_namessignature(object = "MEDIPSset")：提取包括染色体内MEDIPS的名




distFile signature(object = "MEDIPSset"): extracts the name of file containing the custom distance weights, if provided
distfile的signature(object = "MEDIPSset")：提取文件包含自定义距离权重的名称，如果提供




distFunction signature(object = "MEDIPSset"): extracts the distance function specified for calculating the coupling factors
distFunctionsignature(object = "MEDIPSset")：提取指定用于计算耦合因素的距离函数




extend signature(object = "MEDIPSset"): extracts the number of bases by which the regions are extended
延长signature(object = "MEDIPSset")：提取由该区域扩展的碱基数量




fragmentLength signature(object = "MEDIPSset"): extracts the estimated fragment length of the DNA fragments
fragmentLengthsignature(object = "MEDIPSset")：提取的DNA片段的片段长度估计




genome_CF signature(object = "MEDIPSset"): extracts the coupling factor at the genomic bins
在基因箱genome_CFsignature(object = "MEDIPSset")：提取耦合系数




genome_chr signature(object = "MEDIPSset"): extracts the chromosome of the genomic bins
genome_chrsignature(object = "MEDIPSset")：提取染色体的基因组箱




genome_name signature(object = "MEDIPSset"): extracts the refernce genome
genome_namesignature(object = "MEDIPSset")：提取refernce基因组




genome_norm signature(object = "MEDIPSset"): extracts the rms values at the genomic bins
在基因组箱中提取genome_normsignature(object = "MEDIPSset")：RMS值




genome_pos signature(object = "MEDIPSset"): extracts the positions of the genomic bins
genome_possignature(object = "MEDIPSset")：提取的基因组箱的位置




genome_raw signature(object = "MEDIPSset"): extracts the raw MeDIP-Seq signals at the genomic bins
genome_rawsignature(object = "MEDIPSset")：MeDIP-seq的原始信号中提取的基因组箱




intercept signature(object = "MEDIPSset"): extracts the intercept value calculated from the calibration curve
拦截signature(object = "MEDIPSset")：提取从校准曲线的截距值计算




number_pattern signature(object = "MEDIPSset"): extracts the total number of sequence pattern
number_patternsignature(object = "MEDIPSset")：序列模式提取的总人数




number_regions signature(object = "MEDIPSset"): extracts the total number of included regions
number_regionssignature(object = "MEDIPSset")：包括区域中提取的总人数




pattern_chr signature(object = "MEDIPSset"): extracts the chromosomes of the sequence pattern
pattern_chrsignature(object = "MEDIPSset")：提取染色体的序列模式




pattern_pos signature(object = "MEDIPSset"): extracts the positions of the sequence pattern
pattern_possignature(object = "MEDIPSset")：序列模式提取的立场




regions_chr signature(object = "MEDIPSset"): extracts the chromosomes of the regions
regions_chrsignature(object = "MEDIPSset")：提取各区域的染色体




regions_start signature(object = "MEDIPSset"): extracts the start positions of the regions
regions_startsignature(object = "MEDIPSset")：提取区域的起始位置




regions_stop signature(object = "MEDIPSset"): extracts the stop positions of the regions
regions_stopsignature(object = "MEDIPSset")：提取的区域停止位置




regions_strand signature(object = "MEDIPSset"): extracts the strand informations of the regions
区域regions_strandsignature(object = "MEDIPSset")：提取钢绞线信息




sample_name signature(object = "MEDIPSset"): extracts the name of the input file
sample_namesignature(object = "MEDIPSset")：提取输入文件名




seq_pattern signature(object = "MEDIPSset"): extracts the sequence pattern (e.g. CpG)
seq_patternsignature(object = "MEDIPSset")：提取序列模式（例如CPG）




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




slope signature(object = "MEDIPSset"): extracts the slope value calculated from the calibration curve
坡signature(object = "MEDIPSset")：提取从校准曲线斜率值计算




MEDIPS.distributeReads signature(object = "MEDIPSset"): help function for distributing the reads over the genome vector
MEDIPS.distributeReadssignature(object = "MEDIPSset")：散发了帮助功能读取以上的基因向量




MEDIPS.transform signature(object = "MEDIPSset"): help function for transforming ams values
MEDIPS.transformsignature(object = "MEDIPSset")：AMS值转化的帮助功能


作者（S）----------Author(s)----------


Lukas Chavez, Joern Dietrich



举例----------Examples----------


showClass("MEDIPSset")

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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