MACPET {MACPET} | R Documentation |
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.
MACPETUlt
runs the whole analysis at once.
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.
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.
ConvertToPE_BAM
Function for converting two separate BAM files into one paired-end BAM file.
AnalysisStatistics
Prints summary of multiple objects.
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.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.