Sites representing the greatest evidence of enrichment for the NR3C1 transcription factor (DCC accession: ENCFF002CFR) for regions chr2:40000000-50000000 and chr3:10000000-13000000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
GRanges containing one entry per site. The peaks are
surronded by ranges present in the dataset
The peaks and ranges have been obtained using an optimal IDR analysis done on all replicates.
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF002CFR)
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_NR3C1_CFR_NarrowPeaks_partial the associate
genomic regions dataset.
findConsensusPeakRegions for extracting regions
sharing the same features in more than one experiment.
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## Loading datasets data(A549_NR3C1_CFQ_NarrowPeaks_partial) data(A549_NR3C1_CFQ_Peaks_partial) data(A549_NR3C1_CFR_NarrowPeaks_partial) data(A549_NR3C1_CFR_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_NR3C1_CFQ_NarrowPeaks_partial) <- rep("NR3C1_CFQ", length(A549_NR3C1_CFQ_NarrowPeaks_partial)) names(A549_NR3C1_CFQ_Peaks_partial) <- rep("NR3C1_CFQ", length(A549_NR3C1_CFQ_Peaks_partial)) names(A549_NR3C1_CFR_NarrowPeaks_partial) <-rep("NR3C1_CFR", length(A549_NR3C1_CFR_NarrowPeaks_partial)) names(A549_NR3C1_CFR_Peaks_partial) <- rep("NR3C1_CFR", length(A549_NR3C1_CFR_Peaks_partial)) ## Calculating consensus regions for chromosome 2 ## with a default region size of 40 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). ## Peaks from both experiments must be present in a region to ## be retained as a consensus region. chrList <- Seqinfo(c("chr2"), c(243199373), NA) findConsensusPeakRegions( narrowPeaks = c(A549_NR3C1_CFQ_NarrowPeaks_partial, A549_NR3C1_CFR_NarrowPeaks_partial), peaks = c(A549_NR3C1_CFQ_Peaks_partial, A549_NR3C1_CFR_Peaks_partial), chrInfo = chrList, extendingSize = 20, expandToFitPeakRegion = TRUE, shrinkToFitPeakRegion = FALSE, minNbrExp = 2, nbrThreads = 1)
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