R语言 ShortRead包 readIntensities()函数中文帮助文档(中英文对照)

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readIntensities(ShortRead)
readIntensities()所属R语言包：ShortRead

                                        Read Illumina image intensity files
                                         阅读Illumina的图像强度文件

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

readIntensities reads image "intensity" files (such as Illumina's _int.txt and (optionally) _nse.txt) into a single object.
readIntensities读取图像的强度“的文件（如Illumina的_int.txt”（可选）_nse.txt）到一个单一的对象。


用法----------Usage----------


readIntensities(dirPath, pattern=character(0), ...)



参数----------Arguments----------

参数：dirPath
Directory path or other object (e.g., SolexaPath) for which methods are defined.
目录路径，或其他对象（例如，SolexaPath）方法被定义。


参数：pattern
A length 1 character vector representing a regular expression to be combined with dirPath, as described below, to match files to be summarized.
一个长度为1的特征向量代表一个正则表达式要结合dirPath，如下所述，以匹配要总结的文件。


参数：...
Additional arguments used by methods.
方法使用额外的参数。


Details

详情----------Details----------

Additional methods are defined on specific classes, see, e.g., SolexaPath.
另一种方法是在特定的类的定义，例如，见SolexaPath。

The readIntensities,character-method contains an argument type that determines how intensities are parsed. Use the type argument to readIntensities,character-method, as described below. All readIntensities,character methods accepts the folling arguments:
readIntensities,character-method包含一个参数type，决定如何解析强度。使用typereadIntensities,character-method参数，如下所述。所有的readIntensities,character方法接受folling参数：




withVariability: Include estimates of variability (i.e., from
withVariability：包括变异的估计（即从




verbose: Report on progress when starting to read each file.
详细：启动时读取每个文件的进展情况的报告。

The supported types and their signatures are:
支持的类型和他们的签名是：

Intensities are read from Illumina _cif.txt and _cnf.txt-style files.  The signature for this method is
强度从Illumina的_cif.txt和_cnf.txt风格的文件读取。此方法的签名

dirPath, pattern=character(0), ..., type="RtaIntensity", lane=integer(0), cycles=integer(0), cycleIteration=1L, tiles=integer(0), laneName=sprintf("L cycleNames=sprintf("C tileNames=sprintf("s_ posNames=sprintf("s_ withVariability=TRUE, verbose=FALSE
dirPath, pattern=character(0), ..., type="RtaIntensity", lane=integer(0), cycles=integer(0), cycleIteration=1L, tiles=integer(0), laneName=sprintf("L cycleNames=sprintf("C tileNames=sprintf("s_ posNames=sprintf("s_ withVariability=TRUE, verbose=FALSE




lane: integer(1) identifying the lane in which
车道：integer(1)识别车道




cycles: integer() enumerating cycles to be
循环：integer()列举周期




cycleIteration: integer(1) identifying the
cycleIteration：integer(1)确定




tiles: integer() enumerating tile numbers to be
瓷砖：integer()枚举瓦数是

posNames:</dt> character() vectors identifying the lane and cycle directories, and the "pos" and tile file names (excluding the ".cif" or ".cnf" extension) to be
posNames：</ DT>character()向量识别车道和循环目录，和“POS”和瓷砖的文件名（不包括“。到岸价格或。CNF的推广）

The dirPath and pattern arguments are combined as list.files(dirPath, pattern), and must identify a single directory. Most uses of this function will focus on a single tile (specified with, e.g., tiles=1L); the laneName, cycleNames, tileNames, and posNames parameters are designed to work with the default Illumina pipeline and do not normally need to be specified.
dirPath和pattern参数相结合，为list.files(dirPath, pattern)，必须确定一个单一的目录。此功能的用途将集中在一个单一的瓷砖（指定）;tiles=1L，laneName，cycleNames，tileNames参数，如posNames设计工作与默认Illumina的管道，通常不需要被指定。

Intensities are read from Solexa _pos.txt, _int.txt.p, _nse.txt.p-style file triplets. The signature for this method is
读取从公司Solexa_pos.txt，_int.txt.p，_nse.txt.p风格的文件三胞胎强度。此方法的签名

dirPath, pattern=character(0), ...,                 type="IparIntensity", intExtension="_int.txt.p.gz", nseExtension="_nse.txt.p.gz", posExtension="_pos.txt", withVariability=TRUE, verbose=FALSE
dirPath, pattern=character(0), ...,                 type="IparIntensity", intExtension="_int.txt.p.gz", nseExtension="_nse.txt.p.gz", posExtension="_pos.txt", withVariability=TRUE, verbose=FALSE

Files to be parsed are determined as, e.g., paste(pattern,           intExtension, sep="").
要解析的文件，例如paste(pattern,           intExtension, sep="")决定。

Intensities are read from Solexa _int.txt and _nse.txt-style files.  The signature for this method is
公司Solexa_int.txt和_nse.txt风格的文件是只读强度。此方法的签名

dirPath, pattern=character(0), ...,                 type="SolexaIntensity", intExtension="_int.txt", nseExtension="_nse.txt", withVariability=TRUE, verbose=FALSE
dirPath, pattern=character(0), ...,                 type="SolexaIntensity", intExtension="_int.txt", nseExtension="_nse.txt", withVariability=TRUE, verbose=FALSE

Files to be parsed are determined as, e.g., paste(pattern,           intExtension, sep="").
要解析的文件，例如paste(pattern,           intExtension, sep="")决定。


值----------Value----------

An object derived from class Intensity.
来自一个对象类Intensity。


作者（S）----------Author(s)----------



Martin Morgan &lt;mtmorgan@fhcrc.org&gt;,
Michael Muratet &lt;mmuratet@hudsonalpha.org&gt; (RTA).




举例----------Examples----------


fl <- system.file("extdata", package="ShortRead")
sp <- SolexaPath(fl)
int <- readIntensities(sp)
int
intensity(int)[1,,]                 # one read[一个读]
intensity(int)[[1:2,,]]         # two reads, as 'array'[两次读取，如“阵列”]
head(rowMeans(intensity(int)))        # treated as 'array'[被视为“阵列”]
head(pData(readInfo(int)))

## Not run: ## RTA Lane 2, cycles 1:80, cycle iteration 1, tile 3[＃运行：＃退火巷2，周期1:80，循环迭代1，3瓦]
int <- readIntensities("Data/Intensities", type="RtaIntensity",
                       lane=2, cycles=1:80, tiles=3)

## End(Not run)[＃结束（不运行）]

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