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 1.40.0

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