calcMeth(MassArray)
calcMeth()所属R语言包：MassArray
Calculate percent methylation
计算％的甲基化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to calculate percent methylation from a collection of peaks corresponding to a single fragment.
函数来计算％甲基峰对应一个单一的片段的集合。
用法----------Usage----------
calcMeth(SNR.list, fragments = rep(1, length(SNR.list)), non.cg.fragments = numeric(0), method = c("weighted", "proportion"), prune.non.cg.peaks = TRUE, na.rm = FALSE)
参数----------Arguments----------
参数：SNR.list
List of signal-to-noise ratios, sorted from low to high MWs, corresponding to the unmethylated and methylated peaks for a given set of fragments
名单的信号信噪比排序，从低到高的分子量，相应的给定一个片段的甲基化和甲基化峰
参数：fragments
List of all fragments contributing to each of the input peaks, automatically defaulting to a single fragment
列出所有作出贡献的每个输入峰的片段，自动默认为一个单一的片段
参数：non.cg.fragments
List of fragments (without CGs) contributing to any of the input peaks, automatically defaulting to numeric(0)
碎片名单（CGS）任何输入峰，自动拖欠numeric(0)
参数：method
Specifies which algorithm to use when calculating percent methylation (either "weighted" or "proportion")
指定使用哪种算法计算％的甲基化（或者"weighted"或"proportion"）
参数：prune.non.cg.peaks
Boolean value determining whether or not to remove non-CG-containing fragments prior to analysis or whether to include them in the calculating model (note that setting this option to FALSE could result in a considerable increase in analytical time); option automatically defaults to TRUE
布尔值，决定是否删除非CG含片段分析前或是否包括在他们的计算模型（注意，将此选项设置为FALSE可能导致在分析时间大大增加）;选项自动默认TRUE
参数：na.rm
Boolean value determing whether or not to return an error on input of any unspecified data (NA), automatically defaulting to FALSE
布尔值的决定是否返回任何未指定的数据输入错误（NA），自动默认为FALSE
Details
详情----------Details----------
Note that the current release of this function performs as expected for the large majority of cases. However, certain complex combinations of peak overlaps are not handled at this time. This may affect data for a minority of points, particularly those containing multiple overlaps with alternative fragments. Please ensure more in-depth review of such loci.
请注意，此功能的当前版本执引号况大部分为预期。然而，某些复杂的组合，高峰期重叠此时不处理。这可能会影响一小点，特别是那些含有多个重叠替代片段的数据。请确保更深入的检讨这些位点。
值----------Value----------
Returns a numerical values corresponding to percent methylation, with 0
返回％甲基相应的数值，0
作者（S）----------Author(s)----------
Reid F. Thompson (<a href="mailto:rthompso@aecom.yu.edu">rthompso@aecom.yu.edu</a>), John M. Greally (<a href="mailto:jgreally@aecom.yu.edu">jgreally@aecom.yu.edu</a>)
参考文献----------References----------
<h3>See Also</h3>
举例----------Examples----------
data(MassArray.example.data)
frags <- MassArray.example.data$fragments.T[[6]]$"MW"
peaks <- findPeaks(frags, unlist(lapply(MassArray.example.data$samples[[1]]$peaks, slot, "MW.actual")))
SNRs <- unlist(lapply(MassArray.example.data$samples[[1]]$peaks[peaks], slot, "SNR"))
frag.list <- list(1:3, 1:3, 1:3, 1:3)
calcMeth(SNRs, fragments=frag.list, method="weighted")
calcMeth(SNRs, fragments=frag.list, method="proportion")
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。
|
发表于 2012-2-26 00:26:14
