isobar-import(isobar)
isobar-import()所属R语言包：isobar
Loading data into IBSpectra objects using readIBSpectra
装入使用readIBSpectra对象的IBSpectra数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Read ibspectra-csv files and peaklist files as an IBSpectra object of type 'type' (see IBSpectra, e.g. iTRAQ4plexSpectra or TMT6plexSpectra). If peaklist.file is missing, it is assumed that id.file contains intensity and m/z columns for the reporter tags.
作为一个类型类型IBSpectra对象（见IBSpectra，如iTRAQ4plexSpectra或TMT6plexSpectra）的阅读ibspectra csv文件和peaklist文件的。如果peaklist.file丢失，这是假设id.file包含强度和记者标记为m / z为列。
用法----------Usage----------
## S4 method for signature 'character,character'
readIBSpectra(type,id.file)
## S4 method for signature 'character,character,character'
readIBSpectra(type, id.file,
peaklist.file,
proteinGroupTemplate = NULL,
mapping.file = NULL,mapping = c(peaklist=1,id=2),
mapping.file.readopts = list(header=TRUE,stringsAsFactors=FALSE,sep=","),
peaklist.format = NULL, id.format = NULL,
fragment.precision = NULL,fragment.outlier.prob = NULL,
revert.titles = FALSE, scan.lines = 0)
参数----------Arguments----------
参数：type
Name of class of new IBSpectra object: iTRAQ4plexSpectra, iTRAQ8plexSpectra, TMT2plexSpectra, or TMT6plexSpectra
类新IBSpectra对象：iTRAQ4plexSpectra，iTRAQ8plexSpectra，TMT2plexSpectra或TMT6plexSpectra名称
参数：id.file
Database search results file in ibspectra.csv or mzIdentML format. See id.format. See the vignette for information on converting Mascot dat and Phenyx pidres files into ibspectra format.
数据库搜索结果ibspectra.csv或mzIdentML格式的文件。看到id.format。看到的信息转换DAT吉祥物和Phenyx pidres文件到ibspectra格式的小插曲。
参数：peaklist.file
Peaklist file, typically in MGF format, see peaklist.format. MGF must be centroid!
peaklist文件，通常在MGF的格式，看到peaklist.format。 MGF的必须是质心！
参数：proteinGroupTemplate
When having technical or biological repeats: First a template protein group is created which uses information from all runs, then this template is applied. It should increase comparability across runs.
当有技术或生物的重复：首先创建模板蛋白质组使用从所有的运行信息，然后应用此模板。它在运行过程应增加可比性。
参数：mapping.file
If defined, spectum titles from the peaklist file are linked to the identifications via this file. This can be used when running HCD runs for quantification and CID runs for identification. See Koecher et al., 2009 for details.
如果定义，spectum从peaklist文件标题链接，通过这个文件的标识。这可用于运行时的量化及识别的CID运行凯康运行。见详情Koecher等。，2009。
参数：mapping
mapping columns of mapping.file.
mapping.file映射列。
参数：mapping.file.readopts
read options for read.table.
read.table读选项。
参数：peaklist.format
"mgf" (Mascot Generic format) or "mcn" (iTracker Machine Readable output). When NULL, it detects the format on file name extension.
“MGF”（吉祥物通用格式）或“MCN”（iTracker智能监控机可读的输出）。 NULL时，它检测到的文件扩展名的格式。
参数：id.format
"ibspectra.csv" or "mzid" (PSI MzIdentML format). When NULL, file format is guessed based on extension.
“ibspectra.csv”或的“mzid”（PSI的MzIdentML格式）。当空，文件格式被猜到的基础上扩展。
参数：fragment.precision
Fragment precision for extraction of reporter tags: for each tag and spectrum the m/z-intensity pair with it's mass closest to the known reporter tag mass is extracted within the window true_mass +/- fragment.precision/2.
记者标签提取的片段精度为：每个标签和频谱的群众最接近的著名记者的标签质量为m / z强度对的窗口true_mass内提取的+ / - fragment.precision / 2。
参数：fragment.outlier.prob
Fragment outlier probability filter: After all m/z-intensity pairs have been extracted, those pairs with the fragment.outlier.prob/2 most unprecise m/z values are filtered out.
片段离群概率过滤：所有的m / z强度对已提取后，过滤掉那些对最unprecise的fragment.outlier.prob / 2 m / z值。
参数：revert.titles
Unescape spectrum titles in identification file. When extracting the DAT file from Mascot web interface, it's spectrum titles are escaped - %20 instead of space, etc. Set revert.titles to TRUE to map these titles to the unescaped MGF titles.
反向转义的频谱识别文件的标题。吉祥物Web界面提取DAT文件时，它的频谱标题逃脱 - 20％，而不是空间，等集revert.titles TRUE映射这些标题转义的MGF的标题。
参数：scan.lines
Read files sequentially scan.lines lines at a time. Can help in case of memory issues, set to 10000 or higher, for example.
读取文件顺序scan.lines行一次。可以设置为10000或更高的内存问题，例如帮助。
作者（S）----------Author(s)----------
Florian P. Breitwieser, Jacques Colinge
参见----------See Also----------
ProteinGroup, IBSpectra, isobar-preprocessing, isobar-analysis, isobar-plots
ProteinGroup，IBSpectra，压线，预处理，分析等压线，等压线图
举例----------Examples----------
data(ibspiked_set1)
# get identifier for Ceruplasmin proteins[获得Ceruplasmin蛋白质的标识符]
ceru.acs <- protein.g(proteinGroup(ibspiked_set1),"CERU")
# create a smaller ibspectra w/ only Ceruplasmins[创建一个较小的W /只Ceruplasmins ibspectra]
ib.ceru <- subsetIBSpectra(ibspiked_set1,protein=ceru.acs,"include")
# write it to a file[写入到一个文件]
tf <- tempfile("isobar")
write.table(as.data.frame(ib.ceru),sep="\t",file=tf)
# read it again into an IBSpectra object[看了一遍到IBSpectra对象]
ib.ceru2 <- readIBSpectra("iTRAQ4plexSpectra",tf,id.format="ibspectra.csv")
ib.ceru2
unlink(tf)
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 22:36:12
