readDesign(HELP)
readDesign()所属R语言包：HELP
Read NimbleGen design files
NimbleGen的设计文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to extract array design information from corresponding files in the Nimblegen .ndf and .ngd formats.
函数来提取相应的文件的NimbleGen。NDF。NGD格式阵列的设计信息。
用法----------Usage----------
readDesign(x, y, z, ...)
参数----------Arguments----------
参数：x
path to the Nimblegen design file (.ndf). Each line of the file is interpreted as a single spot on the array design. If it does not contain an absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. Alternatively, x can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). file can also be a complete URL.
NimbleGen的设计文件（NDF）的路径。文件的每一行被解释为单点阵列设计上。如果它不包含一个绝对路径，文件名是相对于当前的工作目录，getwd()。波浪线扩展进行支持的地方。另外，x可以是一个可读的连接将打开阅读如有必要，如果在函数调用结束时关闭。 file也可以是一个完整的URL。
参数：y
path to the Nimblegen gene descriptions file (.ngd). Each line of the file is interpreted as a single locus. If it does not contain an absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. Alternatively, y can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). file can also be a complete URL.
NimbleGen的基因描述文件的路径（NGD）。文件的每一行被解释为一个单一的轨迹。如果它不包含一个绝对路径，文件名是相对于当前的工作目录，getwd()。波浪线扩展进行支持的地方。另外，y可以是一个可读的连接将打开阅读如有必要，如果在函数调用结束时关闭。 file也可以是一个完整的URL。
参数：z
object in which to store design information from files. Can be an ExpressionSet, in which case design information will be stored in featureData.
对象存储文件的设计信息。可以ExpressionSet，在这种情况下设计的信息将被储存在featureData。
参数：...
Arguments to be passed to methods (see readDesign-methods):
被传递到方法的参数（见readDesign-methods）：
path a character vector containing a single full path name to which filenames will be appended. If NULL, filenames (x and y) are treated as is.
path字符向量包含一个单一的完整路径名，文件名将追加。如果NULL，文件名（x和y）作为是治疗。
comment.char character: a character vector of length one containing a single character or an empty string (default is "\#"). Use "" to turn off the interpretation of comments altogether.
comment.char性格特征向量的长度为一包含单个字符或一个空字符串（默认为"\#"）。使用""完全关闭评论的解释。
sep the field separator character (default is "\t"). Values on each line of the file are separated by this character. If sep = "" the separator is "white space", that is one or more spaces, tabs, newlines or carriage returns.
sep字段分隔符（默认是"\t"）。文件的每一行的值是通过这个角色分离。如果sep = ""分隔符是“白色空间”，这是一个或多个空格，制表符，换行符或回车。
quote the set of quoting characters (default is "\""). To disable quoting altogether, use quote = "". See scan for the behavior on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified.
quote引号字符集（默认是"\""）。完全禁用引用，使用quote = ""。看到scan引号中嵌入引号的行为。只考虑读的性格，这是所有这些，除非colClasses指定的列引用。
eSet ExpressionSet input (default is new("ExpressionSet")) in which to store design information in featureData
eSetExpressionSet输入（默认为new("ExpressionSet")），其中存储在featureData设计信息
\dots other arguments to be passed to read.table. See read.table.
\dots可以通过read.table其他参数。看到read.table。
值----------Value----------
Returns an ExpressionSet filled with featureData containing the following featureColumns:
返回ExpressionSet充满featureData含有下列featureColumns：
参数：<span class="option">SEQ_ID</span>
a vector of characters with container IDs, linking each probe to a parent identifier
向量的容器ID字符，每个探针连接到父标识符
参数：<span class="option">PROBE_ID</span>
a vector of characters containing unique ID information for each probe
含有独特的ID信息，每个探针的字符向量
参数：<span class="option">X</span>
vector of numerical data determining x-coordinates of probe location on chip
确定探针在芯片上的位置的x坐标的数值数据向量
参数：<span class="option">Y</span>
vector of numerical data determining y-coordinates of probe location on chip
确定芯片上的探针位置的y坐标的数值数据向量
参数：<span class="option">TYPE</span>
a vector of characters defining the type of probe, e.g. random background signals ("RAND") or usable data ("DATA").
确定探针类型，如字符向量随机背景信号（"RAND"）（"DATA"）可用的数据。
参数：<span class="option">CHR</span>
a matrix of characters containing unique ID and chromosomal positions for each container
每个容器包含独特的ID和染色体位置的字符矩阵
参数：<span class="option">START</span>
a matrix of characters containing unique ID and chromosomal positions for each container
每个容器包含独特的ID和染色体位置的字符矩阵
参数：<span class="option">STOP</span>
a matrix of characters containing unique ID and chromosomal positions for each container
每个容器包含独特的ID和染色体位置的字符矩阵
参数：<span class="option">SIZE</span>
a matrix of characters containing unique ID and chromosomal positions for each container
每个容器包含独特的ID和染色体位置的字符矩阵
参数：<span class="option">SEQUENCE</span>
a vector of characters containing sequence information for each probe
一个包含每个探针的序列信息的字符向量
参数：<span class="option">WELL</span>
a vector of characters containing multiplex well location for each probe (if present in design files)
的向量（如目前在设计文件中含有多个井位每个探针的字符）
作者（S）----------Author(s)----------
Reid F. Thompson (<a href="mailto:rthompso@aecom.yu.edu">rthompso@aecom.yu.edu</a>)
参见----------See Also----------
readDesign-methods, read.table
readDesign-methods，read.table
举例----------Examples----------
#demo(pipeline, package="HELP")[演示（管道，包=“帮助”）]
chr <- rep("chr1", 500)
start <- (1:500)*200
stop <- start+199
x <- 1:500
seqids <- sample(1:50, size=500, replace=TRUE)
cat("#COMMENT\nSEQ_ID\tCHROMOSOME\tSTART\tSTOP\n", file="./read.design.test.ngd")[评论\ nSEQ_ID \ tCHROMOSOME \个tstart \ tSTOP \ N“，”文件=“。/ read.design.test.ngd）]
table.ngd <- cbind(seqids, chr, start, stop)
write.table(table.ngd, file="./read.design.test.ngd", append=TRUE, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
cat("#COMMENT\nSEQ_ID\tX\tY\tPROBE_ID\tCONTAINER\tPROBE_SEQUENCE\tPROBE_DESIGN_ID\n", file="./read.design.test.ndf")[评论\ nSEQ_ID \ TX \ TY \ tPROBE_ID \ tCONTAINER \ tPROBE_SEQUENCE \ tPROBE_DESIGN_ID \ N“文件=”。/ read.design.test.ndf“）]
sequence <- rep("NNNNNNNN", 500)
table.ndf <- cbind(seqids, x, x, x, x, sequence, x)
write.table(table.ndf, file="./read.design.test.ndf", append=TRUE, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
x <- readDesign("./read.design.test.ndf", "./read.design.test.ngd")
seqids[1:10]
pData(featureData(x))$"SEQ_ID"[1:10]
#rm(table.ngd, table.ndf, chr, start, stop, x, seqids, sequence)[RM（table.ngd，table.ndf，CHR，启动，停止，X，seqids，序列）]
#file.remove("./read.design.test.ngd")[file.remove（“。/ read.design.test.ngd”）]
#file.remove("./read.design.test.ndf")[file.remove（“。/ read.design.test.ndf”）]
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 21:37:52
