R: Find all genes associated with a genomic range
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Qianhui ▴ 10
@qianhui-16128
Last seen 11 months ago
Australia

Hi all,

I have found around 300 differentially methylated regions (DMRs) between my sample groups in my DNA methylation array analysis, but I didn't found a suitable R package for annotated these regions. I have used matchGenes function in bumphunter package, it matched each region to the nearest gene next to the region. However, I want to find the details of all the genes that potentially associated with each region, are there any other annotation packages for this purpose? Thank you so much!

annotation • 290 views
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@kevin
Last seen 2 hours ago
Republic of Ireland

Hi,

I believe the code that I provide on Biostars will help, in this regard: How to extract the list of genes from TCGA CNV data

That is an adaptation of Listing 11 from Tiago Silva's work on F1000: TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

Kevin

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Hi Kevin, sorry for my late reply. Great answer, thanks for your help!

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