A549_CTCF_MYN_Peaks_partial {consensusSeekeR} | R Documentation |
Sites representing the greatest evidence of enrichment for the CTCF transcription factor (DCC accession: ENCFF000MYN) for regions chr1:246000000-249250621 and chr10:10000000-12500000 from the Encyclopedia of DNA Elements (ENCODE) data (Dunham I et al. 2012).
data(A549_CTCF_MYN_Peaks_partial)
A GRanges
containing one entry per site.
The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYN)
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_MYN_NarrowPeaks_partial
the associate
genomic regions dataset.
findConsensusPeakRegions
for extracting regions
sharing the same features in more than one experiment.
## 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 chromosomes 1 ## 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). ## A peak from both experiments must be present in a region to ## be retained as a consensus region. chrList <- Seqinfo(c("chr1"), c(249250621), 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 = 20, expandToFitPeakRegion = FALSE, shrinkToFitPeakRegion = FALSE, minNbrExp = 2, nbrThreads = 1)