An R-package for binding site analysis of ChIA-PET data.

Description

The MACPET package can be used for general analysis of paired-end (PET) data like ChIA-PET. MACPET currently implements the following four stages: Linker filtering (stage 0), mapping to the reference genome (stage 1), PET classification (stage 2) and peak-calling (stage 3). All of the MACPET stages can be run at once, or separately. In stage 0, MACPET identifies the linkers in the fastq files and classifies the reads as usable, chimeric or ambiguous. Usable reads are considered in the subsequent stages. In stage 1, MACPET maps the usable reads to the reference genome using bowtie and produces a paired-end BAM file. This BAM file is further used in stage 2 to classify the PETs as self-ligated/intra- or inter-chromosomal. Self-ligated PETs are used in stage 3 for the identification of significant peaks. In stage 3, MACPET segments the genome into regions and applies 2D mixture models for identifying candidate peaks using skewed generalized students-t distributions (SGT). It then uses a local poisson model for finding significant binding sites. MACPET is mainly written in C++, and it supports the BiocParallel package.

MACPET main function

MACPETUlt runs the whole analysis at once.

MACPET classes

PSelf

S4 class for Self-ligated PETs.

PSFit

S4 class for Self-ligated PETs after peak-calling.

PInter

S4 class for Inter-chromosomal PETs.

PIntra

S4 class for Intra-chromosomal PETs.

MACPET methods

plot

Method for plotting different objects.

summary

Method for summarizing different objects.

TagsToGInteractions

Method for converting Tags to GInteractions class.

PeaksToGRanges

Method for converting peaks to GRanges class.

exportPeaks

Method for exporting peaks in cvs file format.

ConvertToPSelf

Method for converting a GInteractions class of Self-ligated PETs to object of PSelf class.

PeaksToNarrowPeak

Method for converting peaks to narrowPeak (BED) format for use in interaction analysis using the MANGO algorithm.

MACPET supplementary functions

ConvertToPE_BAM

Function for converting two separate BAM files into one paired-end BAM file.

AnalysisStatistics

Prints summary of multiple objects.

MACPET sample data

SampleChIAPETData.bam

Sample ChIA-PET data.

SampleChIAPETDataRead_1.bam

First reads from the sample ChIA-PET data.

SampleChIAPETDataRead_2.bam

Second reads from the sample ChIA-PET data.

MACPET_pinterData.rda

Sample PInter data.

MACPET_pintraData.rda

Sample PIntra data.

MACPET_pselfData.rda

Sample PSelf data.

MACPET_psfitData.rda

Sample PSFit data.

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.