Description Details Author(s) References See Also

`PSFit`

class in a S4 class which
inherits from the
`GInteractions`

class and it contains Self-ligated
PETs from ChIA-PET experiment and information about the
genome of the data. Furthermore it also contains the following in the
`metadata`

field:

`Self_info`

Counts statistics for the total PETs, total regions and total Peaks in each chromosome.

`SLmean`

The mean size of the PETs in the data.

`MaxSize`

Maximum size of self-ligated PETs.

`MinSize`

Minimum size of self-ligated PETs.

`Classification.Info`

A matrix with information for the Data-row ID, region ID and Peak ID (0 represent noise) of each peak in the data.

`Peaks.Info`

Information for each peak found by the peak-calling algorithm:

`Chrom`

The chromosome which the peak belongs to.

`Region`

The region which the peak belongs to.

`Peak`

The peak ID (a region might have more than one peaks).

`Pets`

Total PETs in the peak.

`Peak.Summit`

Summit of the peak.

`Up.Summit`

Summit of the left-stream PETs.

`Down.Summit`

Summit of the right-stream PETs.

`CIQ.Up.start`

Start of the 95 Quantile confidence interval for the left-stream PETs.

`CIQ.Up.end`

End of the 95 Quantile confidence interval for the left-stream PETs.

`CIQ.Up.size`

Size of the 95 Quantile confidence interval for the left-stream PETs.

`CIQ.Down.start`

Start of the 95 Quantile confidence interval for the right-stream PETs.

`CIQ.Down.end`

End of the 95 Quantile confidence interval for the right-stream PETs.

`CIQ.Down.size`

Size of the 95 Quantile confidence interval for the right-stream PETs.

`CIQ.Peak.size`

Size of the Peak based on the interval (CIQ.Up.start,CIQ.Down.end).

`sdx`

The standard deviation of the upstream PETs.

`lambdax`

The skewness of the upstream PETs.

`sdy`

The standard deviation of the downstream PETs.

`lambday`

The skewness of the downstream PETs.

`lambdaUp`

The expected number of PETs in the left-stream Peak region by random chance.

`FoldEnrichUp`

Fold enrichment for the left-stream Peak region.

`p.valueUp`

p-value for the left-stream Peak region.

`lambdaDown`

The expected number of PETs in the right-stream Peak region by random chance.

`FoldEnrichDown`

Fold enrichment for the right-stream Peak region.

`p.valueDown`

p-value for the right-stream Peak region.

`p.value`

p-value for the Peak (p.valueUp*p.valueDown).

`FDRUp`

FDR correction for the left-stream Peak region.

`FDRDown`

FDR correction for the right-stream Peak region.

`FDR`

FDR correction for the Peak.

`PSFit`

class is created by the
`MACPETUlt`

function at Stage 3.

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

Vardaxis I, DrablĂ¸s F, Rye M and Lindqvist BH (2018). *MACPET: Model-based Analysis for ChIA-PET*.
To be published.

`AnalysisStatistics`

,`plot`

,
`summary`

, `MACPETUlt`

,
`exportPeaks`

, `PeaksToGRanges`

,
`TagsToGInteractions`

, `PeaksToNarrowPeak`

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