Probabilistic inference of ChIP-seq
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Documentation for package ‘PICS’ version 2.49.0
Help Pages
-- B --
| bam2gr | Pre-process bam files |
-- C --
| candidate.region | Identify candidate regions |
| chromosome | Generics associated with pics classes |
| chromosome-method | PICS class |
| chromosome-method | Generics associated with pics classes |
| chromosome-method | picsError class |
| chromosome-method | List of PICS objects |
| code | Generics associated with pics classes |
| code-method | PICS class |
| code-method | picsError class |
| code-method | List of PICS objects |
-- D --
| delta | Generics associated with pics classes |
| delta-method | PICS class |
| delta-method | Generics associated with pics classes |
| delta-method | picsError class |
| delta-method | List of PICS objects |
-- K --
| K | Generics associated with pics classes |
| K-method | PICS class |
| K-method | picsError class |
| K-method | List of PICS objects |
-- L --
| length-method | List of PICS objects |
| length-method | Classes and functions to segment the genome in candidate regions |
-- M --
| makeGRangesOutput | Export a PICS object to GRanges |
| map | Classes and functions to segment the genome in candidate regions |
| map-method | Classes and functions to segment the genome in candidate regions |
| maxRange | Generics associated with pics classes |
| maxRange-method | PICS class |
| maxRange-method | picsError class |
| maxRange-method | List of PICS objects |
| minRange | Generics associated with pics classes |
| minRange-method | PICS class |
| minRange-method | picsError class |
| minRange-method | List of PICS objects |
| mu | Generics associated with pics classes |
| mu-method | PICS class |
| mu-method | Generics associated with pics classes |
| mu-method | picsError class |
| mu-method | List of PICS objects |
-- P --
| PICS | Estimation of binding site positions |
| pics-class | PICS class |
| pics-generics | Generics associated with pics classes |
| picsError-class | picsError class |
| picsFDR | Estimate the FDR |
| picsList-class | List of PICS objects |
| plot-FDR | Plot PICS FDR |
| plot-method | Plot PICS FDR |
| plot-method | Plot methods for PICS objects |
| plot-pics | Plot methods for PICS objects |
-- S --
| score | Generics associated with pics classes |
| score-method | PICS class |
| score-method | Generics associated with pics classes |
| score-method | picsError class |
| score-method | List of PICS objects |
| scoreForward | Generics associated with pics classes |
| scoreForward-method | PICS class |
| scoreForward-method | Generics associated with pics classes |
| scoreForward-method | picsError class |
| scoreForward-method | List of PICS objects |
| scoreReverse | Generics associated with pics classes |
| scoreReverse-method | PICS class |
| scoreReverse-method | Generics associated with pics classes |
| scoreReverse-method | picsError class |
| scoreReverse-method | List of PICS objects |
| se | Generics associated with pics classes |
| se-method | PICS class |
| se-method | Generics associated with pics classes |
| se-method | picsError class |
| se-method | List of PICS objects |
| seF | Generics associated with pics classes |
| seF-method | PICS class |
| seF-method | Generics associated with pics classes |
| seF-method | picsError class |
| seF-method | List of PICS objects |
| segChrRead | Segmentation of paired-end sequencing data |
| segmentPICS | Segment the genome into candidate regions |
| segReads | Classes and functions to segment the genome in candidate regions |
| segReads-class | Classes and functions to segment the genome in candidate regions |
| segReadsGeneric | Perform genome segmentation depending |
| segReadsList | Classes and functions to segment the genome in candidate regions |
| segReadsList-class | Classes and functions to segment the genome in candidate regions |
| segReadsListPE | Class and methods for list of candidate regions from paired-end data |
| segReadsListPE-class | Class and methods for list of candidate regions from paired-end data |
| segReadsPE | Classe and methods for candidate regions from paired-end data |
| segReadsPE-class | Classe and methods for candidate regions from paired-end data |
| seR | Generics associated with pics classes |
| seR-method | PICS class |
| seR-method | Generics associated with pics classes |
| seR-method | picsError class |
| seR-method | List of PICS objects |
| setParaEM | List of parameters for the EM algorithm that can be used as an argument of PICS. |
| setParaPrior | List of parameters that can be used as an argument of PICS. |
| show-method | PICS class |
| show-method | picsError class |
| show-method | List of PICS objects |
| show-method | Classes and functions to segment the genome in candidate regions |
| sigmaSqF | Generics associated with pics classes |
| sigmaSqF-method | PICS class |
| sigmaSqF-method | Generics associated with pics classes |
| sigmaSqF-method | picsError class |
| sigmaSqF-method | List of PICS objects |
| sigmaSqR | Generics associated with pics classes |
| sigmaSqR-method | PICS class |
| sigmaSqR-method | Generics associated with pics classes |
| sigmaSqR-method | picsError class |
| sigmaSqR-method | List of PICS objects |
| summary-method | PICS class |
| summary-method | List of PICS objects |
| summary-method | Classes and functions to segment the genome in candidate regions |
| summarySeg | Summarize segmentList objects |
-- W --
| w | Generics associated with pics classes |
| w-method | PICS class |
| w-method | picsError class |
| w-method | List of PICS objects |
-- misc --
| [-method | List of PICS objects |
| [-method | Classes and functions to segment the genome in candidate regions |
| [-method | Class and methods for list of candidate regions from paired-end data |
| [[-method | List of PICS objects |
| [[-method | Classes and functions to segment the genome in candidate regions |
| [[-method | Class and methods for list of candidate regions from paired-end data |