| as.list-method | Estimation of binding site positions |
| bam2gr | pre-process bam files |
| candidate.region | Segmentation of paired-end sequencing data |
| chromosome | The pics class |
| chromosome-method | The pics class |
| chromosome-method | The pics class |
| chromosome-method | The pics class |
| code | Estimation of binding site positions |
| code-method | Estimation of binding site positions |
| coerce | Estimation of binding site positions |
| coerce-method | Estimation of binding site positions |
| delta | The pics class |
| delta-method | The pics class |
| delta-method | The pics class |
| delta-method | The pics class |
| density-method | The pics class |
| FDR | FDR plot for PICS |
| K | Estimation of binding site positions |
| K-method | Estimation of binding site positions |
| length | The pics class |
| length-method | Segment the genome into candidate regions |
| length-method | The pics class |
| makeRangedDataOutput | Create a RangedData object from a PICS output |
| map | Segment the genome into candidate regions |
| map-method | Segment the genome into candidate regions |
| maxRange | Estimation of binding site positions |
| maxRange-method | Estimation of binding site positions |
| minRange | Estimation of binding site positions |
| minRange-method | Estimation of binding site positions |
| mu | The pics class |
| mu-method | The pics class |
| mu-method | The pics class |
| mu-method | The pics class |
| newPics | The pics class |
| newPics-method | The pics class |
| newPicsError | The pics class |
| newPicsError-method | The pics class |
| newPicsList | The pics class |
| newPicsList-method | The pics class |
| PICS | Estimation of binding site positions |
| pics | Estimation of binding site positions |
| pics-class | Estimation of binding site positions |
| picsError | The pics class |
| picsError-class | The pics class |
| picsFDR | Estimate the FDR. |
| picsList | The pics class |
| picsList-class | The pics class |
| plot-method | Estimation of binding site positions |
| plot-method | FDR plot for PICS |
| score | Estimation of binding site positions |
| score-method | The pics class |
| score-method | The pics class |
| score-method | The pics class |
| scoreForward | Estimation of binding site positions |
| scoreForward-method | Estimation of binding site positions |
| scoreReverse | Estimation of binding site positions |
| scoreReverse-method | Estimation of binding site positions |
| se | The pics class |
| se-method | The pics class |
| se-method | The pics class |
| se-method | The pics class |
| seF | The pics class |
| seF-method | The pics class |
| seF-method | The pics class |
| seF-method | The pics class |
| segChrRead | Segmentation of paired-end sequencing data |
| segmentPICS | Segment the genome into candidate regions |
| segReads | Segment the genome into candidate regions |
| segReads-class | Segment the genome into candidate regions |
| segReadsGeneric | Segment the genome into candidate regions |
| segReadsList | Segment the genome into candidate regions |
| segReadsList-class | Segment the genome into candidate regions |
| segReadsListPE | List of segReadsPE objects |
| segReadsListPE-class | List of segReadsPE objects |
| segReadsPE | Class to store post-segmentation result |
| segReadsPE-class | Class to store post-segmentation result |
| seR | The pics class |
| seR-method | The pics class |
| seR-method | The pics class |
| seR-method | The pics class |
| setParaEM | Function that returns a list of parameters for the EM algorithm that can be used as an argument of PICS. |
| setParaPrior | Function that returns a list of parameters that can be used as an argument of PICS. |
| show | show PICS |
| show-method | show PICS |
| show-methods | show PICS |
| sigmaSqF | Estimation of binding site positions |
| sigmaSqF-method | Estimation of binding site positions |
| sigmaSqR | Estimation of binding site positions |
| sigmaSqR-method | Estimation of binding site positions |
| summary | summary PICS |
| summary-method | summary PICS |
| summary-methods | summary PICS |
| summarySeg | Summarize a segReadsList object. |
| w | The pics class |
| w-method | The pics class |
| w-method | The pics class |
| w-method | The pics class |
| wigDensity | Estimation of binding site positions |
| wigDensity-method | Estimation of binding site positions |
| %in%-method | Segment the genome into candidate regions |
| [-method | Segment the genome into candidate regions |
| [-method | The pics class |
| [-method | List of segReadsPE objects |
| [[-method | Segment the genome into candidate regions |
| [[-method | The pics class |
| [[-method | List of segReadsPE objects |