To annotate a list of KEGG compounds to the KEGG pathways where they are involved I used the R package KEGGREST from Bioconductor.
library(KEGGREST) So, having a list of KEGG compounds saved in a character vector like kegg_compounds, we use the method keggGet in batches of maximum 10 compounds to annotate them.
The following (rudimentary) code, queries the database in batches of ten compounds fiddling a list (pathways) where it creates an entry per pathway and updates the field compounds with the compounds from kegg_compounds for each pathway.
In the HELIX project we decided to use residuals instead of M values for the methylation analyses. So, how we get the residuals of a basic lineal model?
Libraries and Data First of all we load the libraries we will use in this test:
library( limma ) # We use lmFit to fit the lineal model library( minfi ) # Methylation data is saved as a GenomicRatioSet library( SmartSVA ) # We want to compute the SVA to correct methylation data library( isva ) # " library( Biobase ) # We will sabe the residuals in an ExpressionSet Once the libraries are loaded we proceed to obtain the methylation data: