How do I know which peak to analyze?
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schaud24 ▴ 10
@schaud24-14468
Last seen 3.8 years ago

Hello, I am rather new to Bioconductor and was wondering what different peaks indicate when analyzing data. For example, I want to obtain the data for the H3K4me3 histone modification for the H1 cell line from Epigenomics Roadmap. 

> annohub = AnnotationHub()
> annohub = subset(annohub, species == "Homo sapiens")
> qhs = query(annohub, c("H3K4me3", "E003"))
> qhs

AnnotationHub with 6 records
# snapshotDate(): 2017-10-27 
# $dataprovider: BroadInstitute
# $species: Homo sapiens
# $rdataclass: BigWigFile, GRanges
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH28880"]]' 

            title                                  
  AH28880 | E003-H3K4me3.broadPeak.gz              
  AH29884 | E003-H3K4me3.narrowPeak.gz             
  AH30934 | E003-H3K4me3.gappedPeak.gz             
  AH32025 | E003-H3K4me3.fc.signal.bigwig          
  AH33057 | E003-H3K4me3.pval.signal.bigwig        
  AH40183 | E003-H3K4me3.imputed.pval.signal.bigwig

I would like to know which peak(s) I would be interested in. Additionally, in what situations would I be interested in the other peaks? Thank you for your help.

bioconductor annotation peaks • 604 views
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@sean-davis-490
Last seen 18 days ago
United States

This isn't really a Bioconductor question, but more related to an understanding of the underlying signal associated with a chip-seq signal. In this case, you might refer to this site:

https://sites.google.com/site/anshulkundaje/projects/encodehistonemods

which implies that H3K4me3 was analyzed using the "gappedPeak" approach.

 

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