Computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data.
Also enables occupancy (overlap) analysis and plotting functions.
Entry Points:
dba: |
| Construct a dba object |
dba.peakset: |
| Add a peakset to, or retrieve a peakset from, a dba object |
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dba.overlap:
| Compute binding site overlaps and/or correlations |
dba.count: |
| Count reads in binding sites |
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dba.contrast: |
| Establish contrast(s) for analysis |
dba.analyze: |
| Execute affinity analysis |
dba.report: |
| Generate report for a contrast analysis |
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dba.plotHeatmap:
| Heatmap plot |
dba.plotPCA: |
| Principal Components plot |
dba.plotBox: |
| Boxplots |
dba.plotMA: |
| MA/scatter plot |
dba.plotVenn: |
| Venn diagram plot |
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dba.show: |
| Show dba metadata |
dba.mask: |
| Mask samples or sites |
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dba.save: |
| Save dba object |
dba.load: |
| Load dba object |