CS7：Genomic coordination的富集性分析（1）
很多人对我的ChIPseeker, clusterProfiler, ggtree等软件包的印象就是：我一搞就自己方方面面都搞了，其实不然，我这人不喜欢重新造轮子，有现成的就懒得搞了，当年看到seq2pathway这个包发表的文章，我就想着，我要试一下，然后写个教程告诉clusterProfiler用户，可以用这个软件来衔接clusterProfiler，这样就可以对测序片段进行功能富集分析，结果发现这包竟然是不能跑，因为它用了绝对路经！！！
于是我怒了，这不就是ChIPseeker + clusterProfiler可以干的事情，而且在打通了ChIPseeker和clusterProfiler的连接之后，应用更广，不受这包人鼠等模式生物的限制。当时为了吐槽，我专门写了个英文博客，然后扔个链接给包作者，现在已经没有这个问题了，然而我们应该用的是ChIPseeker + clusterProfiler。
我很少吐槽别人的包，但槽点太雷人的时候，必须还是要来一发的，比如《R包辣鸡之CorMut》，已经刷新我们的下限。
I found a Bioconductor package, seq2pathway, that can apply functional analysis to NGS data. It consists of two components, seq2gene and gene2pathway. seq2gene converts genomic coordination to genes while gene2pathway performs functional analysis at gene level.
I think it would be interesting to incorporate seq2gene with clusterProfiler. But it fail to run due to it call absolute path of python installed in the author’s computer.
THIS should never be happened in a Bioconductor package since Bioconductor requires every package to have a least one vignette and runnable examples in man files. It turns out that there is no runnable example in either the vignette or man files. This package was compiled successfully in all platforms but it actually can only be run in windows platform with python installed exactly in the same path of the author. I don’t know why Bioconductor core team didn’t detect this issue when reviewing this package and why reviewers of Bioinformatics didn’t test the package.
I modified ‘C:/Python27/python’, to ‘python’. But it still throw error:
This is due to the author used ‘\\‘ as folder separator which is Windows platform specific.
command <- paste("C:/Python27/python ", tempdir(),"\\",name,sep="")AND I found that there are many ‘\\‘ in the source code.
So I gave up to try this package and reinvented the wheel.
It’s not difficult to implement a seq2gene function using internal functions already available in my package ChIPseeker. It only took me half hour and was available since version 1.5.5. （2015年6月29日，ChIPseeker+clusterProfiler合体已经存在两年多了）
seq2gene provided by ChIPseeker considers host gene (exon/intron), promoter region and flanking gene from intergenomic region.
With ChIPseeker, user can annotates genomic coordination by nearest gene, host gene, flanking genes or consider all of them by seq2gene and performs GO/KEGG/DO/Reactome analysis with clusterProfiler/DOSE/ReactomePA at gene level. A scenario can be found in Bioconductor support site, that used ChIPseeker to retrieve 5 genes flanking of each enhancer followed by GO analysis.
Note:
seq2pathway, https://github.com/Bioconductor-mirror/seq2pathway, version 1.1.2, access date 21 Aug, 2015
Citation
Yu G, Wang LG and He QY*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383.