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 |