PSFit-class {MACPET} | R Documentation

## PSFit S4 Class

### Description

`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.

### Details

`PSFit` class is created by the `MACPETUlt` function at Stage 3.

### Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

### References

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

### See Also

`AnalysisStatistics`,`plot`, `summary`, `MACPETUlt`, `exportPeaks`, `PeaksToGRanges`, `TagsToGInteractions`, `PeaksToNarrowPeak`

[Package MACPET version 1.14.0 Index]