Entering edit mode
12.5 years ago
dutta.tridib
•
0
Hello, I am very new to this area/field of study and my background is not biology. But I need to download data from LGRC database which contains data regarding DNA methylation (charm normalized ? a term unknown to me ). The matrix of data I am looking is a matrix whose rows are methylation values of genes and columns are from patients (with COPD, ILD or CLTR).
Is there a tool / script available which will extract these information from LGRC database ? Any help regarding this would be greatly appreciated.
Thanks
Does the data portal introduction video help? https://www.lung-genomics.org/auth/login?service=https%3a%2f%2fwww.lung-genomics.org%2fresearch%2f If that doesn't help, sometimes you can email the db maintainers & ask for more information about their data structure -- it may help you parse it.
Also, CHARM is an R package. http://www.biostars.org/post/show/11293/identify-differentially-methylated-regions-from-medip-tiling-array-data/
http://www.biostat.jhsph.edu/~maryee/charm/