MACPET: An R-package for binding site analysis of ChIA-PET data.
In IoannisVardaxis/MACPET: Model based analysis for paired-end data
Description
MACPET main function
MACPET classes
MACPET methods
MACPET supplementary functions
MACPET sample data
Author(s)
References
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
PSelfS4 class for Self-ligated PETs.
PSFitS4 class for Self-ligated PETs after peak-calling.
PInterS4 class for Inter-chromosomal PETs.
PIntraS4 class for Intra-chromosomal PETs.
GenomeMapS4 class for the interactions found in the data.
MACPET methods
plotMethod for plotting different objects.
summaryMethod for summarizing different objects.
TagsToGInteractionsMethod for converting Tags to
GInteractions class.
PeaksToGRangesMethod for converting peaks to
GRanges class.
exportPeaksMethod for exporting peaks in cvs file format.
ConvertToPSelfMethod for converting a GInteractions class of
Self-ligated PETs to object of PSelf class.
GetSignInteractionsMethod for subseting the significant interactions of a GenomeMap object.
GetShortestPathMethod for finding the shortest path between two peaks given a set of interactions.
PeaksToNarrowPeakMethod 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_BAMFunction for converting two separate BAM files into one paired-end BAM file.
AnalysisStatisticsPrints summary of multiple
objects.
MACPET sample data
SampleChIAPETData.bamSample ChIA-PET data.
SampleChIAPETDataRead_1.bamFirst reads from the sample ChIA-PET data.
SampleChIAPETDataRead_2.bamSecond reads from the sample ChIA-PET data.
MACPET_pinterData.rdaSample PInter data.
MACPET_pintraData.rdaSample PIntra data.
MACPET_pselfData.rdaSample PSelf data.
MACPET_psfitData.rdaSample PSFit data.
MACPET_GenomeMapData.rdaSample 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.
IoannisVardaxis/MACPET documentation built on Aug. 9, 2019, 12:11 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description MACPET main function MACPET classes MACPET methods MACPET supplementary functions MACPET sample data Author(s) References
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
PSelfS4 class for Self-ligated PETs.
PSFitS4 class for Self-ligated PETs after peak-calling.
PInterS4 class for Inter-chromosomal PETs.
PIntraS4 class for Intra-chromosomal PETs.
GenomeMapS4 class for the interactions found in the data.
MACPET methods
plotMethod for plotting different objects.
summaryMethod for summarizing different objects.
TagsToGInteractionsMethod for converting Tags to
GInteractionsclass.PeaksToGRangesMethod for converting peaks to
GRangesclass.exportPeaksMethod for exporting peaks in cvs file format.
ConvertToPSelfMethod for converting a
GInteractionsclass of Self-ligated PETs to object ofPSelfclass.GetSignInteractionsMethod for subseting the significant interactions of a
GenomeMapobject.GetShortestPathMethod for finding the shortest path between two peaks given a set of interactions.
PeaksToNarrowPeakMethod 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_BAMFunction for converting two separate BAM files into one paired-end BAM file.
AnalysisStatisticsPrints summary of multiple objects.
MACPET sample data
SampleChIAPETData.bamSample ChIA-PET data.
SampleChIAPETDataRead_1.bamFirst reads from the sample ChIA-PET data.
SampleChIAPETDataRead_2.bamSecond reads from the sample ChIA-PET data.
MACPET_pinterData.rdaSample
PInterdata.MACPET_pintraData.rdaSample
PIntradata.MACPET_pselfData.rdaSample
PSelfdata.MACPET_psfitData.rdaSample
PSFitdata.MACPET_GenomeMapData.rdaSample
GenomeMapdata.
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.