MACPET {MACPET} | R Documentation

## 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.

[Package MACPET version 1.0.0 Index]