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| as.list,AlignedRead-method | A function to read in Aligned Short Reads |
| basesCovered | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| coerce,AlignedRead,GenomeData-method | A function to read in Aligned Short Reads |
| combineLanes | Combine or subsample short read alignment locations |
| contextDistribution | Tabulate peak locations according to genomic context |
| copyIRanges | Associate ranges to coverage. |
| copyIRangesbyChr | Associate ranges to coverage. |
| coverageplot | Plot coverage on a small interval. |
| cstest | A test ChIP-Seq dataset |
| densityCorr | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| diffPeakSummary | A function to identify and produce summary statistics for differentially expressed peaks. |
| estimate.mean.fraglen | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,AlignedRead-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,GenomeData-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,IntegerList-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,list-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,RangedData-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| estimate.mean.fraglen,RangesList-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| extendReads | A function to extend short reads. |
| genomic_exons | (Deprecated) Functions that compute genomic regions of interest. |
| genomic_introns | (Deprecated) Functions that compute genomic regions of interest. |
| genomic_regions | (Deprecated) Functions that compute genomic regions of interest. |
| laneSubsample | Combine or subsample short read alignment locations |
| readReads | A function to read in Aligned Short Reads |
| sparse.density | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks. |
| subsetSummary | Compute summaries for cumulative subsets of a short-read data set. |