Genomic regions representing the greatest evidence of enrichment for the FOSL2 transcription factor (DCC accession: ENCFF000MZT) for regions chr1:249120200-249250621 and chr10:1-370100 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
GRanges containing one entry per genomic regions. Each row
GRanges has a name which represent the name of the experiment.
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MZT)
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_FOSL2_01_Peaks_partial the associate
findConsensusPeakRegions for extracting regions
sharing the same features in more than one experiment.
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## Loading datasets data(A549_FOSL2_01_NarrowPeaks_partial) data(A549_FOSL2_01_Peaks_partial) data(A549_FOXA1_01_NarrowPeaks_partial) data(A549_FOXA1_01_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_FOXA1_01_Peaks_partial) <- rep("FOXA1_01", length(A549_FOXA1_01_Peaks_partial)) names(A549_FOXA1_01_NarrowPeaks_partial) <- rep("FOXA1_01", length(A549_FOXA1_01_NarrowPeaks_partial)) names(A549_FOSL2_01_Peaks_partial) <-rep("FOSL2_01", length(A549_FOSL2_01_Peaks_partial)) names(A549_FOSL2_01_NarrowPeaks_partial) <- rep("FOSL2_01", length(A549_FOSL2_01_NarrowPeaks_partial)) ## Calculating consensus regions for chromosome 10 only ## with a default region size of 200 bp (2 * extendingSize) ## which is not extended to include all genomic regions. ## A peak from both experiments must be present in a region to ## be retained as a consensus region. chrList <- Seqinfo("chr10", 135534747, NA) findConsensusPeakRegions( narrowPeaks = c(A549_FOXA1_01_NarrowPeaks_partial, A549_FOSL2_01_NarrowPeaks_partial), peaks = c(A549_FOXA1_01_Peaks_partial, A549_FOSL2_01_Peaks_partial), chrInfo = chrList, extendingSize = 100, expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = TRUE, minNbrExp = 2, nbrThreads = 1)
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