Question: Filtering Go Terms By Evidence Code And Apply A Semantic Similarity Measure
2
gravatar for jfertaj
6.2 years ago by
jfertaj90
United Kingdom
jfertaj90 wrote:

Hello,

I have a list of different pathways and I would like to filter this pathways based on the semantic similarity (Resnik distance, e.g) of the GO terms associated to each gene. However, I would like to consider only the GO terms with evidence codes related to experimental support. Could you tell me any approach, mainly in R/Bioconductor. I have tested GOsemsim but I am not able to filter firs the evidence codes.

Thanks a lot

bioconductor go • 1.7k views
ADD COMMENTlink written 6.2 years ago by jfertaj90

GO evidence codes are certainly in Biomart as I use custom tables from ensembl biomart for this (or via the Perl API). Regarding R, BiomaRt would be a good place to check but I do not use it: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html

ADD REPLYlink written 6.2 years ago by Alastair Kerr5.2k

Ok, I'll try also with Biomart, but I just realised that GOsemsim has an option to drop the evidence codes that you are not interested in

ADD REPLYlink written 6.2 years ago by jfertaj90
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