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

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Documentation for package ‘soGGi’ version 1.41.0

• 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