MEDIPS.methylProfiling(MEDIPS)
MEDIPS.methylProfiling()所属R语言包：MEDIPS
Funtion calculates mean methylation values (rpm, rms) and ams values, ratios, variances, and pvalues comparing two MEDIPS SETs for user supplied regions of interests (ROIs) or genome wide frames.
：funtion计算平均甲基化值（每分钟转速，RMS）和AMS值，比率，方差，pvalues比较两个区域的用户提供的利益（投资回报）或全基因组框架MEDIPS集。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
In order to compare two different conditions, first you have to create and process two MEDIPS SETs. For the identification of DMRs, MEDIPS provides two alternative approaches. First, you can specify pre-defined regions of interest (ROIs). Second, MEDIPS offers the possibility to calculate differential methylation for genome wide frames. The function calculates summarized methylation values for the defined ROIs. Here, these are the mean values for both provided MEDIPS SETs as well as the ratio of means. Moreover, for each ROI, MEDIPS calculates p-values by comparing the set of rpm values (or rms values, respectively) within the ROI of the one MEDIPS SET against the set of rpm values (or rms values, respectively) within the ROI of the second MEDIPS SET using R's wilcox.test and t.test functions. Additionally, it is recommended (but not necessary) to provide background data from an INPUT experiment (that is sequencing of none-enriched DNA fragments). By providing an INPUT data set, MEDIPS additionally returns mean INPUT rpm values for the specified ROIs. Please note, the function takes a long processing time when called for genome wide short windows (up to days).
为了比较两种不同的条件，首先你必须创建和处理两个MEDIPS集。 MEDIPS对于识别DMRs，提供了两种可供选择的办法。首先，你可以指定预先定义的兴趣区域（ROI）。第二，MEDIPS计算全基因组帧差的甲基化提供了可能性。函数的计算定义的ROI总结的甲基化值。在这里，这些都是为同时提供MEDIPS的平均值设置以及手段的比例。此外，每个投资回报率，MEDIPS计算p值，通过比较内对转速值（或有效值，分别）设置一个MEDIPS的投资回报率的投资回报率在转速值（或有效值，分别）第二MEDIPS使用R的wilcox.test和t.test功能，设置。此外，它推荐（但不是必需的），提供从输入实验（即没有丰富的DNA片段的测序）的背景资料。通过提供一个输入数据集，MEDIPS额外收益的意思是指定的投资回报的输入转速值。请注意，功能基因组短而宽的窗口（天）调用时需要很长的处理时间。
用法----------Usage----------
MEDIPS.methylProfiling(data1 = NULL, data2 = NULL, input = NULL, ROI_file = NULL, frame_size = NULL, math = "mean", step = NULL, select = 2, chr = NULL, transf=T)
参数----------Arguments----------
参数：data1
has to be a MEDIPS SET object (the control data)
是MEDIPS集对象（控制数据）
参数：data2
has to be a MEDIPS SET object (the treatment data)
是MEDIPS集对象（处理数据）
参数：input
has to be a MEDIPS SET object (the input data)
是MEDIPS集对象（输入数据）
参数：ROI_file
instead of processing genome wide frames using the parameters frame_size and step, here you can provide a file containing predefined ROIs.
处理全基因组框架使用参数frame_size和步骤的，而不是在这里你可以提供一个文件，其中包含预定的投资回报。
参数：frame_size
Besides summarizing methylation values for pre-defined ROIs, MEDIPS allows for calculating mean methylation values along the full chromosomes. For this, you have to specify a desired frame size here.
除了MEDIPS总结甲基预先定义的ROI值，允许沿整个染色体的平均甲基化值计算。对于这一点，你必须指定所需的帧大小。
参数：math
default=mean; Here, you can specify other functions available in R for sumarizing values like median or sum.
默认值=的意思，在这里，你可以指定在R提供的其他功能，如中位数或总和值sumarizing。
参数：step
The step parameter defines the number of bases by which the frames are shifted along the chromosome. If you e.g. set the frame_size parameter to 500 and the step parameter to 250, then MEDIPS calculates mean methylation values for overlapping 500bp windows, where the size of the overlap will be 250bp for all neighbouring windows.
步骤参数定义的帧沿染色体转移的碱基。如果你如设置的frame_size的参数为500和250步参数，，然后MEDIPS计算意味着重叠500bp的窗口，重叠的大小，将所有邻国窗口250bp甲基值。
参数：select
can be either 1 or 2. If set to 1, the variance, ratio, and p-values will be calculated based on the rpm values; if set to 2, the rms values will be considered instead.
可以是1或2。如果设置为1，方差，比率，p值将转速值的基础上计算;如果设置为2，RMS值将被视为代替。
参数：chr
only the specified chromosome will be evaluated (e.g. chr1)
只有指定的染色体将被评估（如chr1）
参数：transf
If set to TRUE, MEDIPS transforms the mean rms and ams values into log2 scale and subsequently transforms their resulting data range into the consistent interval $[0,1000]$ before finally stored.
如果设置为TRUE，MEDIPS转换成规模的log2平均有效值和AMS值和随后转换成一致区间[0,1000]，最后才存储其产生的数据范围。
值----------Value----------
参数：chr
the chromosome of the ROI
投资回报率的染色体
参数：start
the start position of the ROI
投资回报率的起始位置
参数：stop
the stop position of the ROI
投资回报率的停止位置
参数：length
the number of genomic bins included in the ROI
基因箱的数量，包括在投资回报率
参数：coupling
the mean coupling factor of the ROI
投资回报率的平均耦合系数
参数：input
the mean reads per million value of the INPUT MEDIPS SET at input (if provided)
平均读取每百万在输入设置的输入MEDIPS的价值（如果提供）
参数：rpm_A
the mean reads per million value for the MEDIPS SET at data1
平均每百万在DATA1 MEDIPS价值读取
参数：rpm_B
the mean reads per million value for the MEDIPS SET at data2
平均每百万在DATA2 MEDIPS价值读取
参数：rms_A
the mean relative mathylation score for the MEDIPS SET at data1
平均在DATA1 MEDIPS相对mathylation得分
参数：rms_B
the mean relative methylation score for the MEDIPS SET at data2
平均在DATA2 MEDIPS相对甲基得分
参数：ams_A
the mean absolute mathylation score for the MEDIPS SET at data1. The ams scores are derived by dividing the mean rms value of the ROI by the mean coupling factor of the ROI before the log2 and interval transformations are performed.
平均为DATA1在设置MEDIPS的绝对mathylation得分。除以平均均方根值的投资回报率的投资回报率平均耦合因素前的log2和执行的时间间隔转换得到本队得分。
参数：ams_B
the mean absolute mathylation score for the MEDIPS SET at data2. The ams scores are derived by dividing the mean rms value of the ROI by the mean coupling factor of the ROI before the log2 and interval transformations are performed.
在DATA2设置MEDIPS的绝对mathylation得分平均为。除以平均均方根值的投资回报率的投资回报率平均耦合因素前的log2和执行的时间间隔转换得到本队得分。
参数：var_A
the variance of the rpm or rms values (please see the parameter select) of the MEDIPS SET at data1
rpm或有效值的MEDIPS（请参阅参数选择）的方差在DATA1
参数：var_B
the variance of the rpm or rms values (please see the parameter select) of the MEDIPS SET at data2
rpm或有效值的MEDIPS（请参阅参数选择）的方差在DATA2
参数：var_co_A
the variance coefficient of the rpm or rms values (please see the parameter select) of the MEDIPS SET at data1
rpm或有效值的变异系数（请参阅参数选择），在DATA1设置MEDIPS
参数：var_co_B
the variance coefficient of the rpm or rms values (please see the parameter select) of the MEDIPS SET at data2
rpm或有效值的变异系数（请参阅参数选择），在DATA2设置MEDIPS
参数：ratio
rpm_A/rpm_B or rms_A/rms_B, respectively (please see the parameter select)
rpm_A / rpm_B或rms_A / rms_B的，分别为（请参阅参数选择）
参数：pvalue.wilcox
the p.value returned by R's wilcox.test function for comparing the rpm values (or rms values, respectively; please see the parameter select) of the MEDIPS SET at data1 and of the MEDIPS SET at data2
p.value返回R的wilcox.test函数的转速值（或有效值，分别比较，请参阅参数选择）在DATA1 MEDIPS的MEDIPS在DATA2
参数：pvalue.ttest
the p.value returned by R's t.test function for comparing the rpm values (or rms values, respectively; please see the parameter select) of the MEDIPS SET at data1 and of the MEDIPS SET at data2
p.value返回R的t.test函数的转速值（或有效值，分别比较，请参阅参数选择）在DATA1 MEDIPS的MEDIPS在DATA2
作者（S）----------Author(s)----------
Joern Dietrich
举例----------Examples----------
library(BSgenome.Hsapiens.UCSC.hg19)
file=system.file("extdata", "MeDIP_hESCs_chr22.txt", package="MEDIPS")
CONTROL.SET = MEDIPS.readAlignedSequences(BSgenome="BSgenome.Hsapiens.UCSC.hg19", file=file)
CONTROL.SET = MEDIPS.genomeVector(data = CONTROL.SET, bin_size = 50, extend = 400)
CONTROL.SET = MEDIPS.getPositions(data = CONTROL.SET, pattern = "CG")
CONTROL.SET = MEDIPS.couplingVector(data = CONTROL.SET, fragmentLength = 700, func = "count")
CONTROL.SET = MEDIPS.calibrationCurve(data = CONTROL.SET)
CONTROL.SET = MEDIPS.normalize(data = CONTROL.SET)
ROI_file = system.file("extdata", "hg19.chr22.txt", package="MEDIPS")
promoter = MEDIPS.methylProfiling(data1 = CONTROL.SET, ROI_file = ROI_file, math = mean, select = 2)
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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。
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发表于 2012-2-26 00:38:12
