aCGH.read.Sprocs(aCGH)
aCGH.read.Sprocs()所属R语言包：aCGH
Create object of class "aCGH" from Sproc files
从SPROC文件创建对象类“aCGH”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads in two-channel Array Comparative Genomic Hybridization Sproc files, flags them for bad quality and missing data, and creates object of class aCGH.
此功能双通道阵列比较基因组杂交SPROC文件中读取，标志为质量差和缺少数据，并创建对象的类aCGH。
用法----------Usage----------
aCGH.read.Sprocs(fnames, latest.mapping.file = NULL, maxsd = 0.2,
minreplic = 2, chrom.remove.threshold = 24,
prop.missing = 0.25, sample.names = fnames,
sample.quality.threshold = 0.4,
cols = c("Log2Rat", "Log2StdDev", "NReplic", "Bad.P"),
unmapScreen=TRUE, dupRemove = TRUE)
参数----------Arguments----------
参数：fnames
a vector of character strings containing the file names of each Sproc data file.
包含每个的SPROC数据文件的文件名字符的字符串向量。
参数：latest.mapping.file
The name of an optional file that contains newer clone mapping different from the clone mapping used at the time when the arrays were created.
一个可选的文件，其中包含新克隆映射当阵列创建时间用来克隆映射不同的名称。
参数：maxsd
maximum of standard deviation of log2 ratios used in pre-filtering.
最大log2比例用于预过滤的标准偏差。
参数：minreplic
minimum number of replicates per clone for a single chip used to calculate the log2 ratios.
每克隆一个单一的芯片用于计算log2比率最低数量的复制。
参数：chrom.remove.threshold
Chromosomes are ordered and numbered as usual, except for X and Y chromosome, which in for Homo sapiens genome have numbers 23 and 24 repsectivelly, in for Mus musculus 20 and 21, etc.
像往常一样的染色体排序和编号，除X和Y染色体，在智人基因组有数字repsectivelly 23日和24日在小家鼠20日和21等，
参数：prop.missing
Clones are screened out and if the proportion missing in the samples is prop.missing they are removed.
克隆被筛选出，如果样品中失踪的比例是prop.missing删除它们。
参数：sample.names
Sample names. If they are missing, the file names are used after stripping the characters after the last dot in the filename if one exists; for example 'myfile.txt' becomes myfile.
样本名。如果他们缺少，使用后剥离后的文件名，如果存在的最后一个点字符的文件名，例如myfile.txt的变成MYFILE。
参数：sample.quality.threshold
Mark those samples that have their proportion of missing values sample.quality.threshold.
标记这些样本有遗漏值sample.quality.threshold比例。
参数：cols
character vector of length 4 containing the following Sproc file column names: log2 ratios, std. deviations of the log2 ratios, number of replicates for each clone and flags for bad clones. Defaults to c("Log2Rat", "Log2StdDev", "NReplic", "Bad.P"). Note that all the whitespace characters in the column names will be replaced with dots.
长度包含以下的的SPROC文件列名4：log2比率，性病的特征向量。 log2比率偏差，数量复制坏克隆，每个克隆和标志。默认为c（“Log2Rat”，“Log2StdDev”，“NReplic”，“Bad.P”）。请注意，列名的所有空白字符将取代点。
参数：unmapScreen
Indicator for whether clones with incomplete mapping information should be removed from the dataset. Note that leaving them in may cause plotting routines fail. Defaults to TRUE
是否映射信息不完全的克隆指标应当从DataSet中删除。请注意，使他们在可能导致图例程失败。默认为true
参数：dupRemove
Indicator for whether clones with duplicate names should be averaged and removed from the dataset leaving only one occurence of each duplicated set.Defaults to TRUE
指标名称重复的克隆是否应平均，并从DataSet中删除，只留下一个的发生每个重复set.Defaults的为TRUE
值----------Value----------
Object of class aCGH.
对象类aCGH。
作者（S）----------Author(s)----------
Jane Fridlyand, Peter Dimitrov
参见----------See Also----------
aCGH
aCGH
举例----------Examples----------
datadir <- system.file("examples", package = "aCGH")
latest.mapping.file <-
file.path(datadir, "human.clones.info.Jul03.txt")
ex.acgh <-
aCGH.read.Sprocs(dir(path = datadir,pattern = "sproc",
full.names = TRUE), latest.mapping.file,
chrom.remove.threshold = 23)
ex.acgh
## Testing if creating the object went right. Should all be true.[＃测试如果创建的对象去。都应该是真实的。]
all(log2.ratios(ex.acgh)[ 1, ] == c(-0.077698 , 0.007389))
clone.name <- "HumArray2H10_T30"
all(log2.ratios(ex.acgh)[ clone.name, ] == c(0.025567 , -0.036908))
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 10:58:21
