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 five stages: Linker filtering (stage 0), mapping to the reference genome (stage 1), PET classification (stage 2), peak-calling (stage 3) and interaction analysis (stage 4). The interaction analysis stage (4) currently supports only intra-chromosomal data. 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. Finally, in stage 4, MACPET uses the peaks from stage 3 as well as the Intra-chromosomal PETs from stage 2 to running an additive interaction-analysis model. 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.

`GenomeMap`

  S4 class for the interactions found in the data.

### 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.

`GetSignInteractions`

  Method for subseting the significant interactions of a `GenomeMap` object.

`GetShortestPath`

  Method for finding the shortest path between two peaks given a set of interactions.

`PeaksToNarrowPeak`

  Method for converting peaks to narrowPeak (BED) format for use in interaction analysis using the MANGO/MICC algorithm. Alternatively the user can run stage 4 at `MACPETUlt`.

### 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.

`MACPET_GenomeMapData.rda`

  Sample `GenomeMap` 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.

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

[Package MACPET version 1.4.0 Index]