A549_FOSL2_01_NarrowPeaks_partial: Genomic regions with the greatest evidence of transcription...

Description Usage Format Source References See Also Examples

Description

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).

Usage

1

Format

A GRanges containing one entry per genomic regions. Each row of GRanges has a name which represent the name of the experiment.

Source

The Encyclopedia of DNA Elements (ENCODE) (DCC accession: ENCFF000MZT)

References

See Also

Examples

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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)

ArnaudDroitLab/consensusSeekeR documentation built on Sept. 2, 2017, 8:25 p.m.