Visulising KEGG pathways using KEGGSOAP - example code
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@michael-watson-iah-c-378
Last seen 7.7 years ago
Dear All Having given a training course in this area earlier this year, I thought I would contribute some sample code on how to visualise microarray data on KEGG pathways using KEGGSOAP. This can be found by going to our webpage (http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml) and clicking on "Sample Code". The code is in three sections. The first simply uses GEOquery and biomaRt to retrieve some Affymetrix array data from GEO and link it to ensembl id using Biomart. NOTE: I sometimes have trouble getting the data from the NCBI servers, and if this step fails, none of the subsequent code will work - please be patient. The second section then downloads some files from the KEGG ftp server, and uses the merge() function to link the array data to the relevant pathways. Finally, the third section uses KEGGSOAP and geneplotter to colour KEGG pathways according to the array values. The code is freely available without guarantee or warranty! Do whatever you like with it, but I would appreciate an acknowledgement in whatever you do. Thanks Mick Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confide...{{dropped:26}}
Pathways geneplotter KEGGSOAP biomaRt GEOquery Pathways geneplotter KEGGSOAP biomaRt • 617 views
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