PSFit-class: PSFit S4 Class

Description Details Author(s) References See Also

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, Drabl<c3><b8>s 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


MACPET documentation built on Nov. 8, 2020, 5:47 p.m.