posToProbeAnno(Ringo)
posToProbeAnno()所属R语言包：Ringo
Function for creating a probeAnno environment
功能创建probeAnno环境
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function allows the user to create a probeAnno environment that holds the mapping between probes on the array and their genomic match position(s). As input, the function takes either a.) one of NimbleGen's POS file or a similar file that holds the mapping of probes to the genome. OR b.) a data.frame holding this information
此功能允许用户创建一个probeAnno环境，保持探针阵列上，其基因组的比赛位置（S）之间的映射。作为输入，该函数。）NimbleGen的POS文件或类似的文件保存探针到基因组的映射。或B）data.frame持有此信息。
用法----------Usage----------
posToProbeAnno(pos, chrNameColumn = "CHROMOSOME",
probeColumn = "PROBE_ID", chrPositionColumn = "POSITION",
lengthColumn = "LENGTH", sep="\t", genome="unknown",
microarrayPlatform="unknown", verbose = TRUE, ...)
参数----------Arguments----------
参数：pos
either a file-name that specifies the path to the POS or other mapping file OR a data.frame holding the mapping
无论是文件名，指定路径到POS或其他映射文件或数据框的映射
参数：chrNameColumn
name of the column in the file or data.frame that holds the chromosome name of the match
名称列在文件或data.frame，认为本场比赛的染色体名称
参数：probeColumn
name of the column that holds the matching probe's unique identifier
持有匹配的探针的唯一标识符列的名称
参数：chrPositionColumn
name of the column that holds the match genomic position/coordinate on the chromosome
列持有比赛基因的位置名称/在染色体上的协调
参数：lengthColumn
name of the column that holds the length of the match position, in case of perfect match should correspond to the sequence length of the probe
列名持有的比赛位置的长度，完美匹配的情况下，应该对应的探针序列长度
参数：sep
string; denotes the seperator between elements in the supplied mappings file pos; passed on to function scan; ignored if pos is not a filename.
串;表示元素之间的分隔符文件中提供的映射pos;功能通过scan;忽略pos如果是不是一个文件名。
参数：genome
string; denotes genome (and assembly) the reporters have been mapped to for this probeAnno object, e.g. "M. musculus (mm9)"
字符串表示基因组（组装）记者已经映射这probeAnno对象，如“M家鼠（MM9）“
参数：microarrayPlatform
string; denotes the commercial or custom microarray platform/design that holds the reporters whose mapping is stored in this probeAnno object, e.g. "NimbleGen MOD SUZ12"
串;表示商业或自定义的芯片平台/设计，拥有记者在存储这probeAnno对象的映射，例如： “NimbleGen的当日SUZ12”
参数：verbose
logical; should progress be written to STDOUT?
逻辑;进步应该被写入到STDOUT？
参数：...
further arguments passed on to function scan, which is used for reading in the file pos.
进一步的参数传递给函数scan，这是用来阅读文件pos。
Details
详情----------Details----------
The default column names correspond to the column names in a NimbleGen POS file.
默认列名对应NimbleGen的POS机文件中的列名。
For custom mappings, using the tools Exonerate, BLAT or MUMmer, the scripts directory of this package holds Perl scripts to generate such a POS file from the respective output files.
对于自定义的映射，使用的工具开脱，BLAT或哑剧演员，这个包的scripts目录持有Perl脚本生成等从各自的输出文件的POS文件。
值----------Value----------
The results is an object of class probeAnno.
结果是一个对象类probeAnno。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
probeAnno-class, scan
probeAnno-class，scan
举例----------Examples----------
exPos <- read.delim(file.path(system.file("exData",package="Ringo"),
"MOD_2003-12-05_SUZ12_1in2.pos"),
header=TRUE,as.is=TRUE)
str(exPos)
exProbeAnno <- posToProbeAnno(exPos,
genome="M. musculus (assembly mm8)",
microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
## is equivalent to [＃相当于]
exProbeAnno2 <- posToProbeAnno(file.path(
system.file("exData",package="Ringo"),"MOD_2003-12-05_SUZ12_1in2.pos"),
genome="M. musculus (assembly mm8)",
microarrayPlatform="NimbleGen 2005-06-17_Ren_MM5Tiling_Set1")
ls(exProbeAnno)
chromosomeNames(exProbeAnno2)
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 2012-2-26 12:58:36
