GOFunction(GOFunction)
GOFunction()所属R语言包：GOFunction
main function of the GO-function package
GO功能包的主要功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The GOFunction function is the main function of the GO-function package and can generate a set of biologically relevant GO terms.
GOFunction功能是GO功能包的主要功能，并能产生一系列生物学相关的GO术语。
用法----------Usage----------
GOFunction(interestGenes, refGenes, organism = "org.Hs.eg.db", ontology = "BP", fdrmethod = "BY", fdrth = 0.05, ppth = 0.05, pcth = 0.05, poth = 0.05, peth = 0.05, bmpSize = 2000, filename = "sigTerm")
参数----------Arguments----------
参数：interestGenes
interestGenes is a set of interesting genes (e.g. differential expressed genes), which should be denoted using the Entrez gene ID.
interestGenes是一组有趣的基因（如微分表达的基因），应使用Entrez基因ID表示。
参数：refGenes
refGenes is the background genes corresponding to the interesting genes, which should be denoted using the Entrez gene ID.
refGenes的背景是有趣的基因，应使用Entrez基因ID表示相应的基因。
参数：organism
The GO-function package can be currently applied to analyse data for 18 organisms and the user should install the corresponding gene annotation package when analysing data for these organisms. The 18 organisms and the corresponding packages are as follows: Anopheles "org.Ag.eg.db", Bovine "org.Bt.eg.db", Canine "org.Cf.eg.db", Chicken "org.Gg.eg.db", Chimp "org.Pt.eg.db", E coli strain K12 "org.EcK12.eg.db", E coli strain Sakai "org.EcSakai.eg.db", Fly "org.Dm.eg.db", Human "org.Hs.eg.db", Mouse "org.Mm.eg.db", Pig "org.Ss.eg.db", Rat "org.Rn.eg.db", Rhesus "org.Mmu.eg.db", Streptomyces coelicolor "org.Sco.eg.db", Worm "org.Ce.eg.db", Xenopus "org.Xl.eg.db", Yeast "org.Sc.sgd.db", Zebrafish "org.Dr.eg.db". The default organism is "org.Hs.eg.db" (Human).
GO功能包目前可以应用于18生物体和这些微生物分析数据时，用户应安装相应的基因注释包分析数据。 18生物体和相应的软件包如下：按蚊“org.Ag.eg.db”，牛“org.Bt.eg.db”，犬“org.Cf.eg.db”的，鸡“ org.Gg.eg.db“，黑猩猩”org.Pt.eg.db“，大肠杆菌菌株K12的的”org.EcK12.eg.db“，大肠杆菌菌株酒井”org.EcSakai.eg.db“ ，飞“org.Dm.eg.db”，人“org.Hs.eg.db”，鼠标“org.Mm.eg.db”，猪“org.Ss.eg.db”，大鼠“org.Rn.eg.db”，猕猴“org.Mmu.eg.db”，链霉菌org.Sco.eg.db“，虫”org.Ce.eg.db“，爪蟾” ; org.Xl.eg.db“酵母”org.Sc.sgd.db“，斑马鱼的”org.Dr.eg.db“。默认organism是的“org.Hs.eg.db”（人类）。
参数：ontology
The default ontology is "BP" (Biological Process). The "CC" (Cellular Component) and "MF" (Molecular Function) ontologies can also be used.
默认ontology是“BP”（生物处理）。也可以用“CC”（蜂窝式元器件）及“MF”（分子功能）本体。
参数：fdrmethod
GO-function provides three p value correction methods: "bonferroni", "BH" and "BY". The default fdrmethod is "BY".
GO功能提供三个P值校正方法：“邦弗朗尼”，“波黑”和“”。 “”是的默认fdrmethod。
参数：fdrth
fdrth is the fdr cutoff to identify statistically significant GO terms. The default is 0.05.
fdrth是FDR截止到确定统计学意义的GO术语。默认是0.05。
参数：ppth
ppth is the significant level to test whether the remaining genes of the ancestor term are enriched with interesting genes after removing the genes in its significant offspring terms. The default is 0.05.
ppth是显着的水平，以测试是否丰富有趣的基因取出后在其显着的后代条款基因的祖先术语的其余基因。默认是0.05。
参数：pcth
pcth is the significant level to test whether the frequency of interesting genes in the offspring terms are significantly different from that in the ancestor term. The default is 0.05.
pcth是显着的水平，以测试是否有趣的基因在后代条款的频率有显着不同的祖先术语的。默认是0.05。
参数：poth
poth is the significant level to test whether the overlapping genes of one term is significantly different from the non-overlapping genes of the term. The default is 0.05.
poth是显着的水平，以测试是否一个术语的重叠基因是从术语的非重叠基因显着不同。默认是0.05。
参数：peth
peth is the significant level to test whether the non-overlapping genes of one term is enriched with interesting genes. The default is 0.05.
peth是显着的水平，以测试是否一个术语的非重叠基因是丰富有趣的基因。默认是0.05。
参数：bmpSize
bmpSize is the width and height of the plot of GO DAG for all statistically significant terms. GO-function set the default width and height of the plot as 2000 pixels in order to clearly show the GO DAG structure. If the GO DAG is very complexity, the user should increase bmpSize. Note: If there is an error at the step of "bmp(filename, width = 2000, ..." when running GO-function, the user should decrease bmpSize.
bmpSize是所有统计学意义上的宽度和高度好DAG的图。 GO-功能设置为2000像素的默认宽度和高度的图，以清楚地表明，GO的DAG结构。如果GO DAG是非常复杂，用户应增加bmpSize。注：如果有一个错误的一步“BMP（文件名，宽度= 2000，...”GO功能运行时，用户应减少bmpSize。
参数：filename
filename is the name of the files saving the table and the GO DAG of all statistically significant terms.
filename文件保存表和所有统计学意义上的好DAG的名称。
值----------Value----------
There are two types of result output of GO-function. The first type is that GO-function saves a table contained all statistically significant terms to a CSV file (e.g. "sigTerm.csv") in the current working folder. This table contains seven columns: goid, name, refnum (the number of the reference genes in a GO term), interestnum (the number of the interesting genes in a GO term), pvalue, adjustp (the corrected p value by the fdr control), FinalResults. The "FinalResults" contains three types: (1) "Local" represents terms removed after treating for local redundancy; (2) "Global" represents terms removed after treating for global redundancy; (3) "Final" represents the remained terms with evidence that their significance should not be simply due to the overlapping genes. GO-function also saves the structure of GO DAG for all statistic significant terms into a plot (e.g. "sigTerm.bmp") in the current working folder. In this plot, "circle", "box" and "rectangle" represent "Local", "Global" and "Final" terms in the table, respectively. The different color shades represent the adjusted p values of the terms.
GO功能的输出结果有两种类型。第一类是GO功能表保存到CSV文件在当前工作文件夹（如“sigTerm.csv”）所载的所有统计学意义。此表包含七列：goid，名称，引用句柄（在GO术语的参考基因的数量），interestnum（有趣的基因在GO术语的数量），pvalue，adjustp（FDR控制纠正P值），FinalResults。 “FinalResults”包含三种类型：（1）“本地”代表本地冗余治疗后删除的条款;（2）“环球”代表全球冗余治疗后，删除的条款;（3）“最终”代表保持的证据表明，其意义不应该只是由于重叠基因。 GO功能，还可以节省好DAG的所有重要条款积成在当前的工作文件夹（如“sigTerm.bmp”）的统计结构。在此图中，“圆”，“盒子”和“矩形”代表“本地”，“环球”和“决赛”表中的条款，分别。不同的颜色深浅代表的条款调整后的P值。
注意----------Note----------
GO-function use the GO data and annotation data from Bioconductor, so the user does not need to update the data manually.
GO-函数使用Bioconductor GO数据和注释数据，因此用户并不需要手动更新数据。
作者（S）----------Author(s)----------
Jing Wang
举例----------Examples----------
data(exampledata)
sigTerm <- GOFunction(interestGenes, refGenes, organism = "org.Hs.eg.db", ontology= "BP", fdrmethod = "BY",
fdrth = 0.05, ppth = 0.05, pcth = 0.05, poth = 0.05, peth = 0.05, bmpSize = 2000, filename="sigTerm")
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。
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发表于 2012-2-25 20:46:57
