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"))
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"]]'
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.