R语言 aCGH包 aCGH.process()函数中文帮助文档(中英文对照)

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aCGH.process(aCGH)
aCGH.process()所属R语言包：aCGH

                                        Process data in aCGH object
                                         在aCGH对象的过程数据

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function takes object of class aCGH, and filters clones based on their mapping information and proportion missing. It also average duplicated clones and reports quality statistic.
此功能类aCGH，并根据他们的映射信息和比例失踪过滤器克隆的对象。它还平均重复克隆和报告的质量统计。


用法----------Usage----------


aCGH.process(aCGH.obj, chrom.remove.threshold = 24,
                 prop.missing = 0.25, sample.quality.threshold = 0.4,
                 unmapScreen=TRUE, dupRemove = TRUE)



参数----------Arguments----------

参数：aCGH.obj
Object of class aCGH
对象的类aCGH


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.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：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(package = "aCGH")
datadir <- paste(datadir, "/examples", sep="")

clones.info <-
      read.table(file = file.path(datadir, "clones.info.ex.txt"),
                 header = TRUE, sep = "\t", quote="", comment.char="")
log2.ratios <-
      read.table(file = file.path(datadir, "log2.ratios.ex.txt"),
                 header = TRUE, sep = "\t", quote="", comment.char="")
pheno.type <- read.table(file = file.path(datadir, "pheno.type.ex.txt"),header = TRUE, sep = "\t", quote="", comment.char="")
ex.acgh <- create.aCGH(log2.ratios, clones.info, pheno.type)
ex.acgh <-
    aCGH.process(ex.acgh, chrom.remove.threshold = 23, prop.missing = .25,
sample.quality.threshold = .4, unmapScreen=TRUE, dupRemove = FALSE)
ex.acgh


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


注：
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