Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
Sites representing the greatest evidence of enrichment for the CTCF transcription factor (DCC accession: ENCFF000MYJ) for regions chr1:246000000-249250621 and chr10:10000000-12500000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
GRanges containing one entry per site.
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYJ)
Dunham I, Kundaje A, Aldred SF, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.
A549_CTCF_MYJ_Peaks_partialthe associate genomic peaks dataset.
findConsensusPeakRegionsfor extracting regions sharing the same features in more than one experiment.
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## Loading datasets data(A549_CTCF_MYJ_NarrowPeaks_partial) data(A549_CTCF_MYJ_Peaks_partial) data(A549_CTCF_MYN_NarrowPeaks_partial) data(A549_CTCF_MYN_Peaks_partial) ## Assigning experiment name to each row of the dataset. ## NarrowPeak and Peak datasets from the same experiment must ## have identical names. names(A549_CTCF_MYJ_Peaks_partial) <- rep("CTCF_MYJ", length(A549_CTCF_MYJ_Peaks_partial)) names(A549_CTCF_MYJ_NarrowPeaks_partial) <- rep("CTCF_MYJ", length(A549_CTCF_MYJ_NarrowPeaks_partial)) names(A549_CTCF_MYN_Peaks_partial) <-rep("CTCF_MYN", length(A549_CTCF_MYN_Peaks_partial)) names(A549_CTCF_MYN_NarrowPeaks_partial) <- rep("CTCF_MYN", length(A549_CTCF_MYN_NarrowPeaks_partial)) ## Calculating consensus regions for chromosome 10 ## with a default region size of 100 bp (2 * extendingSize) ## which is extended to include all genomic regions for the closest ## peak to the median position of all peaks included in the region (for each ## experiment). ## A peak from both experiments must be present in a region to ## be retained as a consensus region. chrList <- Seqinfo(c("chr10"), c(135534747), NA) findConsensusPeakRegions( narrowPeaks = c(A549_CTCF_MYJ_NarrowPeaks_partial, A549_CTCF_MYN_NarrowPeaks_partial), peaks = c(A549_CTCF_MYJ_Peaks_partial, A549_CTCF_MYN_Peaks_partial), chrInfo = chrList, extendingSize = 50, expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = TRUE, minNbrExp = 2, nbrThreads = 1)
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