PSFit-class: PSFit S4 Class
In IoannisVardaxis/MACPET: Model based analysis for paired-end data

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.