# Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

## Documentation for package ‘soGGi’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | Join, subset and manipulate ChIPprofile objects
c-method | Join, subset and manipulate ChIPprofile objects
cbind-method | Join, subset and manipulate ChIPprofile objects
chipExampleBig | Example ChIPprofiles
ChIPprofile | The soggi function and ChIPprofile object.
ChIPprofile-ChIPprofile | The soggi function and ChIPprofile object.
ChIPprofile-class | The soggi function and ChIPprofile object.
findconsensusRegions | Plot coverage of points or regions.
groupByOverlaps | Create GRangeslist from all combinations of GRanges
ik_Example | Example Ikaros peaksets
ik_Profiles | Example Ikaros signal over peaksets
log-method | Arithmetic operations
log2-method | Arithmetic operations
makeMotifScoreRle | PWM hits and motif scores as an RLElist
mean-method | Arithmetic operations
normalise | Normalise ChIPprofiles
normalise-method | Normalise ChIPprofiles
normalise.ChIPprofile | Normalise ChIPprofiles
normaliseQuantiles | Normalise quantile
normaliseQuantiles-method | Normalise quantile
normaliseQuantiles.ChIPprofile | Normalise quantile
Ops-method | Arithmetic operations
orientBy | Set strand by overlapping or nearest anchor GRanges
plotRegion | Plot regions
plotRegion-method | Plot regions
plotRegion.ChIPprofile | Plot regions
pwmCov | Example motif coverage
pwmToCoverage | PWM hits and motif scores as an RLElist
rbind-method | Join, subset and manipulate ChIPprofile objects
regionPlot | The soggi function and ChIPprofile object.
singleGRange | A single GRange
soggi | The soggi function and ChIPprofile object.
summitPipeline | Plot coverage of points or regions.
[[-method | Join, subset and manipulate ChIPprofile objects