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.

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.