A549_CTCF_MYJ_NarrowPeaks_partial: Sites with the greatest evidence of transcription factor...

Description Usage Format Source References See Also Examples

Description

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).

Usage

1

Format

A GRanges containing one entry per site.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MYJ)

References

See Also

A549_CTCF_MYJ_NarrowPeaks_partial

Examples

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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)

consensusSeekeR documentation built on May 31, 2017, 11:18 a.m.

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