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对接通用的go注释 #44

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GuangchuangYu opened this issue Jan 4, 2024 · 2 comments
Open

对接通用的go注释 #44

GuangchuangYu opened this issue Jan 4, 2024 · 2 comments

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@GuangchuangYu
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  1. 标准化read.gafread.blast2go的输出为data.frame

我们现在有read.gafread.blast2go,两个函数的输出不太一致,改成都输出data.frame,两column名字和顺序固定下来,分别是Gene, GO,事实上这两种数据都应该有GO分支的信息,有的话,加第三个Column,Ontology,标准化为MF, CC和BP,像blast2go的输出有GO Domain就是这个信息。

当前read.gaf()有额外的输出,这一块分离出来。

  1. 支持data.frame为输入

那么标准化上面两函数之后,如果我们能支持data frame来分析的话,那这两函数的输出就能直接用了,以及可以让用户自己提供data.frame,能直接用。

这个只要衔接godata这个函数,让OrgDb支持输入一个data.frame就行了。里面调用的函数,调整一下。如此一来,GOSemSim就打通了,因为上面的东西,全部都基于godata()的输出。

@GuangchuangYu
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godata() 函数还应该对接一下gson对象,https://cran.r-project.org/web//packages/gson/index.html

@GuangchuangYu
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EggNOG的解析也是需要的, YuLab-SMU/ProjectYulab#16.

GuangchuangYu added a commit that referenced this issue Jan 16, 2024
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