outputToCGHregions(ADaCGH2)
outputToCGHregions()所属R语言包：ADaCGH2
ADaCGH2 output as input to CGHregions
作为ADaCGH2输出输入到CGHregions
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Convert ADaCGH2 output to a data frame that can be used as input for CGHregions.
可以用来作为CGHregions的输入到一个数据框转换ADaCGH2输出。
用法----------Usage----------
outputToCGHregions(output, directory = getwd())
参数----------Arguments----------
参数：output
The name of the output from a call to a pSegment function.
pSegment函数调用输出的名称。
参数：directory
The directory where the initial data transformation and the analysis have been carried out. It is a lot better if you just work on a single directory for a set of files. Otherwise, unless you keep very carefull track of where you do what, you will run into trouble.
已经进行了目录的初始数据转换和分析。这是好多了，如果你只是在一个单一的一组文件目录。否则，除非你把你做的轨道非常carefull，你会遇到麻烦。
值----------Value----------
A data frame of 4 + k columns that can be used as input to the CGHregions function. The first four columns are the probe name, the chromosome, the position and the position. The last k columns are the calls for the k samples.
的4个数据框+ KCGHregions函数的输入可以使用的列。前四列探测器名称，染色体中的地位和位置。在过去的k列k个样本的呼声。
注意----------Note----------
This function does NOT check if the calls are meaningfull. In particular, you probably do NOT want to use this function when pSegment has been called using merging = "none".
这个函数不检查如果调用meaningfull。特别是，你可能不希望使用此功能，当pSegment已被称为使用merging = "none"。
作者（S）----------Author(s)----------
Ramon Diaz-Uriarte <a href="mailto:rdiaz02@gmail.com">rdiaz02@gmail.com</a>
参见----------See Also----------
pSegment
pSegment
举例----------Examples----------
## Create a temp dir for storing output.[＃创建一个临时目录，用于存储输出。]
## (Not needed, but cleaner).[＃（不是必需的，但清洁剂）。]
dir.create("ADaCGH2_cghreg_example_tmp_dir")
originalDir <- getwd()
setwd("ADaCGH2_cghreg_example_tmp_dir")
Sys.sleep(1)
snowfallInit(universeSize = 2, typecluster = "SOCK")
## To speed up R CMD check, we do not use inputEx1, but a much smaller[＃为了加快R CMD检查，我们不使用inputEx1，但要小得多]
## data set. When you try the examples, you might one to use[＃设置数据。当您尝试的例子，你可能要使用的]
## inputEx1 instead.[＃inputEx1代替。]
## Not run: [＃无法运行：]
fname <- list.files(path = system.file("data", package = "ADaCGH2"),
full.names = TRUE, pattern = "inputEx1")
## End(Not run)[＃结束（不运行）]
fname <- list.files(path = system.file("data", package = "ADaCGH2"),
full.names = TRUE, pattern = "inputEx2")
tableChromArray <- inputDataToADaCGHData(filename = fname)
hs_mad.out <- pSegmentHaarSeg("cghData.RData",
"chromData.RData", merging = "MAD")
forcghr <- outputToCGHregions(hs_mad.out)
if(require(CGHregions)) {
regions1 <- CGHregions(forcghr)
regions1
}
### Explicitly stop cluster[＃明确停止聚类]
sfStop()
### Clean up (DO NOT do this with objects you want to keep!!!)[＃清理（不跟你想保留的对象！！）]
load("chromData.RData")
load("posData.RData")
load("cghData.RData")
delete(cghData); rm(cghData)
delete(posData); rm(posData)
delete(chromData); rm(chromData)
unlink("chromData.RData")
unlink("posData.RData")
unlink("cghData.RData")
unlink("probeNames.RData")
lapply(hs_mad.out, delete)
rm(hs_mad.out)
### Try to prevent problems in R CMD check[＃尽量避免问题在R加利福尼亚检查]
### (As a regular user, most likely you do not need this)[＃（作为一个普通用户，最有可能你并不需要这种）]
Sys.sleep(2)
detach("package:rlecuyer", unload = TRUE)
### Delete all files and temp dir[＃删除所有文件和temp目录]
setwd(originalDir)
Sys.sleep(2)
unlink("ADaCGH2_cghreg_example_tmp_dir", recursive = TRUE)
Sys.sleep(2)
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 11:03:28
