GOSemSim

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Hi, See in the picture what I tried, can't follow the code to find the error. Where the error should be I've tried to manually run the other lines to...

mauritsunkel

buildGOmap issues, therefore 2 suggestions

2

@GuangchuangYu , @huerqiang At the Bioconductor support forum an issue/error was reported regarding the function `buildGOmap`: https://support.bioconductor.org/p/9156358/ I had a quick look at it, and it seems this is because...

guidohooiveld

对接通用的go注释

2

1. 标准化`read.gaf`和`read.blast2go`的输出为data.frame 我们现在有[read.gaf](https://github.com/YuLab-SMU/GOSemSim/blob/devel/R/parseGAF.R)和[read.blast2go](https://github.com/YuLab-SMU/GOSemSim/blob/devel/R/readBlast2go.R)，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。 2. 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](https://github.com/YuLab-SMU/GOSemSim/blob/devel/R/godata.R)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

1. 现在支持非常多的物种，因为不是内置支持，而是先外部处理OrgDb，准备好GO注释。 + OrgDb可以通过AnnotationHub获得，如果没有的话，也可以自己通过AnnotationForge构建，另外[AnnotationHub检索回来的OrgDb也可以打包为R包](https://support.bioconductor.org/p/92004/)，以供后续使用。 + 支持GAF文件 （衔接蛋白质组注释，. + Blast2GO输出 + 支持用户输入data.frame, . 即便是用户自己注释的新基因组，也能够分析，少去了搞OrgDb的门槛。 2. 基于信息含量的几种方法是我用C++重写的，后来又有[@alyst优化](https://github.com/GuangchuangYu/GOSemSim/pull/1)，现在的速度更快。 3. 实现了新方法TCSS 4. 支撑其它包的语义相似性度量，包括disease ontology, human phenotype ontology, mouse phenotype ontology, Medical Subject Headings等。 +...

GuangchuangYu

need to recompute IC after dropping evidence codes

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Hi, thank you for this package. It is very useful! This is not a bug but a potential issue. IC is calculated on the full set of Gene-GO annotations at...

dkainer

mgeneSim with Resnik measure produces incorrect results

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Hi, I'm trying to use GOSemSim to compute pairwise similarity scores for a large set of genes and it seems that the Resnik measure at least is incorrect because the...

deniseduma

GOSemSim package download error

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Although I downloaded the GOSemSim package to R (V4.1.2) without any problems with the codes below, I cannot find the package in the library after the download is finished. What...

kahvecirem

results from function `mgoSim` based on "Wang" method

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I have found that different types of `hsGO` have no effect on the similarity results. R codes as below: ```R go1

DeepColin

Running calculations in parallel

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Is it possible to replace the `sapply` and `apply`'s in the code with `BiocParallel::bplapply`? For example `mclusterSim` becomes really slow when the number of clusters / the size of the...

y1zhou

Information Content/goSim could be calculated for more GO terms?

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Dear authors, I am trying to calculate semantic similarity between some GO terms based on the information content methods. ```R # GO.db retrieved by 2020-09-10, Bioconductor version 3.12 atGO

dorrenasun