Package 'r3Cseq'

Title: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Description: This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.
Authors: Supat Thongjuea, MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, UK <[email protected]>
Maintainer: Supat Thongjuea <[email protected]> or <[email protected]>
License: GPL-3
Version: 1.53.0
Built: 2024-11-30 03:40:43 UTC
Source: https://github.com/bioc/r3Cseq

Help Index

calculate read per million (RPM) for replicates analysis

Description

Normalize 3C-Seq data by transforming raw reads to read per million per each region for replication analysis

Usage

calculateBatchRPM(object,normalized_method=c("powerlawFittedRPM","normalRPM"))

Arguments

object

r3CseqInBatch object

normalized_method

character. method of normalization (default=powerlawFittedRPM)

Author(s)

S. Thongjuea

See Also

calculateRPM, expRPM contrRPM

Examples

#See the vignette

calculate read per million (RPM)

Description

Normalize 3C-Seq data by transforming raw reads to read per million per each region

Usage

calculateRPM(object,normalized_method=c("powerlawFittedRPM","normalRPM"))

Arguments

object

r3Cseq object

normalized_method

character. method of normalization (default=powerlawFittedRPM)

Author(s)

S. Thongjuea

See Also

contrRPM, expRPM, calculateBatchRPM

Examples

#See the vignette

This method has been removed.

Description

This method has been removed.

get interaction regions from the control

Description

get all identified interaction regions from the control

Usage

contrInteractionRegions(object)

Arguments

object

r3Cseq or r3CseqInBatch object

Value

The candidate interaction regions show in the IRange object

Author(s)

S. Thongjuea

See Also

expInteractionRegions, getInteractions

Examples

#See the vignette

Accessors for the 'contrRawData' slot of a r3Cseq object.

Description

The 'contrRawData' slot of hold the raw aligned reads data in the GRanges object.

Usage

## S4 method for signature 'r3Cseq'
contrRawData(object)
## S4 replacement method for signature 'r3Cseq'
contrRawData(object) <- value

Arguments

object

r3Cseq object

value

a GRanges object of aligned reads

Author(s)

S. Thongjuea

See Also

expRawData

Examples

#See the vignette

get read count per region for the control

Description

get the read count per region for the control

Usage

contrReadCount(object)

Arguments

object

r3Cseq object

Author(s)

S. Thongjuea

See Also

expReadCount, getReadCountPerRestrictionFragment

Examples

#See the vignette

get read per million (RPM) for the control

Description

get the normalized 3C-seq data (RPM) for the control

Usage

contrRPM(object)

Arguments

object

r3Cseq or r3CseqInBatch object

Author(s)

S. Thongjuea

See Also

calculateRPM, expRPM

Examples

#See the vignette

Rebase The Restriction Enzyme Database

Description

The database includes all restriction enzyme information from the REBASE database.

References

http://rebase.neb.com/rebase/rebase.html

This method has been removed.

Description

This method has been removed.

get interaction regions from the experiment

Description

get identified interaction regions from the experiment

Usage

expInteractionRegions(object)

Arguments

object

r3Cseq or r3CseqInBatch object

Value

The candidate interaction regions show in the IRange object

Author(s)

S. Thongjuea

See Also

getInteractions, contrInteractionRegions

Examples

#See the vignette

export interaction regions to the 'bedGraph' format

Description

export interaction regions from RagedData to the bedGraph format, which suitable for uploading to the UCSC genome browser

Usage

export3Cseq2bedGraph(object,datatype=c("rpm","read_count"))

Arguments

object

r3Cseq object, The object might contain the interaction regions generated by function getInteractions

datatype

read_count : read count per restriction fragment rpm : normalized read per million per restriction fragment

Value

The text file in 'bedGraph' format

Author(s)

S. Thongjuea

See Also

exportInteractions2text

Examples

#See the vignette

export the interaction signal from the raw reads to the 'bedGraph' format

Description

export interaction regions signal to the bedGraph format, which suitable for uploading to the UCSC genome browser

Usage

export3CseqRawReads2bedGraph(object)

Arguments

object

r3Cseq object

Value

The text file in 'bedGraph' format

Author(s)

S. Thongjuea

See Also

exportInteractions2text, export3Cseq2bedGraph,

Examples

#See the vignette

export identified interaction regions to the tab separated format for replicates analysis

Description

export interaction regions from RagedData to the tab separated format for replicates analysis

Usage

exportBatchInteractions2text(object)

Arguments

object

r3CseqInBatch object

Value

The text file in the tab separated format

Author(s)

S. Thongjuea

See Also

export3Cseq2bedGraph, exportInteractions2text

Examples

#See the vignette

export identified interaction regions to the tab separated format

Description

export interaction regions from RagedData to the tab separated format

Usage

exportInteractions2text(object)

Arguments

object

r3Cseq object

Value

The text file in the tab separated format

Author(s)

S. Thongjuea

See Also

export3Cseq2bedGraph

Examples

#See the vignette

Accessors for the 'expRawData' slot of a r3Cseq object.

Description

The 'expRawData' slot of hold the raw aligned reads data in the GRanges object.

Usage

## S4 method for signature 'r3Cseq'
expRawData(object)
## S4 replacement method for signature 'r3Cseq'
expRawData(object) <- value

Arguments

object

r3Cseq object

value

a GRanges object of aligned reads

Author(s)

S. Thongjuea

See Also

expRawData

Examples

#See the vignette

get read count per region for the experiment

Description

get the read count per region for the experiment

Usage

expReadCount(object)

Arguments

object

r3Cseq

Author(s)

S. Thongjuea

See Also

contrReadCount, getReadCountPerRestrictionFragment

Examples

#See the vignette

get read per million (RPM) for the experiment

Description

get the normalized 3C-seq data (RPM) for the experiment

Usage

expRPM(object)

Arguments

object

r3Cseq or r3CseqInBatch

Author(s)

S. Thongjuea

See Also

calculateRPM, contrRPM

Examples

#See the vignette

generate reports for analysis results from r3Cseq

Description

generate reports for analysis results from r3Cseq, the report contains all plots in one pdf file and a text separated out put file.

Usage

generate3CseqReport(obj)

Arguments

obj

r3Cseq or r3CseqInBatch object

Value

The text file in the tab separated format and the pdf file of all plots

Author(s)

S. Thongjuea

See Also

exportInteractions2text plotOverviewInteractions, plotInteractionsPerChromosome, plotInteractionsNearViewpoint

Examples

#See the vignette

calculate z-score, assign p-value and q-value for each interaction region for replicates data sets

Description

Calculate z-score, assign p-value and q-value to each interaction regions for replicates data sets

Usage

getBatchInteractions(object,method=c("union","intersection"),smoothing.parameter=0.1,fdr=0.05)

Arguments

object

r3Cseq object

method

character. The method for combining biological replicates for 3C-Seq analysis (default = "union")

smoothing.parameter

A level at which cubic smoothing spline for the spar (see vsmooth.spline) input parameter. Must be in (0.06,0.4] (default=0.1)

fdr

A level at which to control the FDR. Must be in (0,1] (default=0.05)

Value

The interaction regions show in the RangedData

Author(s)

S. Thongjuea

See Also

getInteractions vsmooth.spline

Examples

#See the vignette

Get aligned reads from the replicates BAM files

Description

Reading in the input BAM files from the 3C-Seq replicates analysis and then save files as the local GRanged object .rData files

Usage

getBatchRawReads(object)

Arguments

object

r3CseqInBatch object

Value

The GRangedData represents the aligned reads from the BAM file

Author(s)

S. Thongjuea

See Also

getRawReads,

Examples

#See the vignette

count reads for replicates analysis

Description

Counts the number of reads from 3C-Seq data per each restriction fragment for replicates analysis

Usage

getBatchReadCountPerRestrictionFragment(object,getReadsMethod = c("wholeReads", "adjacentFragmentEndsReads"),
			nFragmentExcludedReadsNearViewpoint=2)

Arguments

object

r3CseqInBatch object

getReadsMethod

character. To count all reads found in the particular restriction fragment uses wholeReads option. To count reads found around the edge of restriction fragment both 5'utr and 3'utr uses adjacentFragmentEndsReads option (default=wholeReads)

nFragmentExcludedReadsNearViewpoint

Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)

Value

The RangedData represents the number of reads per each restriction fragment

Author(s)

S. Thongjuea

See Also

getReadCountPerWindow, getReadCountPerRestrictionFragment

Examples

#See the vignette

count reads per window size for replicates analysis

Description

Counts the number of reads from 3C-Seq data per each window size for replicates analysis

Usage

getBatchReadCountPerWindow(object,windowSize=5e3,nFragmentExcludedReadsNearViewpoint=2,mode=c("non-overlapping", "overlapping"))

Arguments

object

r3CseqInBatch object

windowSize

Numeric. non-overlapping window size for counting reads (default=5e3)

nFragmentExcludedReadsNearViewpoint

Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)

mode

character. The window-based modes analysis (default="non-overlapping")

Value

The RangedData represents the number of reads per each window size

Author(s)

S. Thongjuea

See Also

getReadCountPerRestrictionFragment, getBatchReadCountPerRestrictionFragment, getReadCountPerWindow,

Examples

#See the vignette

identified significant interaction regions for RefSeq genes

Description

Get a list of genes that contain strong interaction signals in the control

Usage

getContrInteractionsInRefseq(obj,cutoff.qvalue=0.05,expanded_upstream=50e3,expanded_downstream=10e3)

Arguments

obj

obj is r3Cseq or r3CseqInBatch object

cutoff.qvalue

Numeric. The cutoff q-value (default=0.05)

expanded_upstream

Numeric. The expanded distance from the upstream of a gene start (default=50e3)

expanded_downstream

Numeric. The expanded distance from the downstream of a gene end (default =10e3)

Value

List of identified genes, which contain strong interaction signals

Author(s)

S. Thongjuea

See Also

getContrInteractionsInRefseq

Examples

# See the vignette

This method has been removed.

Description

This method has been removed.

identified significant interaction regions for RefSeq genes

Description

Get a list of genes that contain strong interaction signals in the experiment

Usage

getExpInteractionsInRefseq(obj,cutoff.qvalue=0.05,expanded_upstream=50e3,expanded_downstream=10e3)

Arguments

obj

obj is r3Cseq or r3CseqInBatch object

cutoff.qvalue

Numeric. The cutoff q-value (default=0.05)

expanded_upstream

Numeric. The expanded distance from the upstream of a gene start (default=50e3)

expanded_downstream

Numeric. The expanded distance from the downstream of a gene end (default =10e3)

Value

List of identified genes, which contain strong interaction signals

Author(s)

S. Thongjuea

See Also

getContrInteractionsInRefseq

Examples

# See the vignette

calculate z-score, assign p-value and q-value for each interaction region

Description

Calculate z-score, assign p-value and q-value to each interaction regions

Usage

getInteractions(object,smoothing.parameter=0.1,fdr=0.05)

Arguments

object

r3Cseq object

smoothing.parameter

A level at which cubic smoothing spline for the spar (see vsmooth.spline) input parameter. Must be in (0.06,0.4] (default=0.1)

fdr

A level at which to control the FDR. Must be in (0,1] (default=0.05)

Value

The interaction regions show in the RangedData

Author(s)

S. Thongjuea

See Also

getBatchInteractions vsmooth.spline

Examples

#See the vignette

Get aligned reads from the BAM file

Description

Reading in the input BAM file and then store it in the GRanged object

Usage

getRawReads(object)

Arguments

object

r3Cseq object

Value

The GRangedData represents the aligned reads from the BAM file

Author(s)

S. Thongjuea

See Also

getBatchRawReads,

Examples

#See the vignette

count reads per resitrcition fragment

Description

Counts the number of reads from 3C-Seq data per each restriction fragment

Usage

getReadCountPerRestrictionFragment(object,getReadsMethod = c("wholeReads", "adjacentFragmentEndsReads"),
			nFragmentExcludedReadsNearViewpoint=2)

Arguments

object

r3Cseq object

getReadsMethod

character. To count all reads found in the particular restriction fragment uses wholeReads option. To count reads found around the edge of restriction fragment both 5'utr and 3'utr uses adjacentFragmentEndsReads option (default=wholeReads)

nFragmentExcludedReadsNearViewpoint

Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)

Value

The RangedData represents the number of reads per each restriction fragment

Author(s)

S. Thongjuea

See Also

getReadCountPerWindow, getBatchReadCountPerRestrictionFragment

Examples

#See the vignette

count reads per window size

Description

Counts the number of reads from 3C-Seq data per each window size

Usage

getReadCountPerWindow(object,windowSize=5e3,nFragmentExcludedReadsNearViewpoint=2,mode=c("non-overlapping"))

Arguments

object

r3Cseq object

windowSize

Numeric. non-overlapping window size for counting reads (default=5e3)

nFragmentExcludedReadsNearViewpoint

Numeric. The number of excluded fragments around the viewpoint, reads found in these fragments will be removed from the analysis (default=2)

mode

character. The window-based modes analysis (default="non-overlapping")

Value

The RangedData represents the number of reads per each window size

Author(s)

S. Thongjuea

See Also

getReadCountPerRestrictionFragment,

Examples

#See the vignette

get the viewpoint of 3C-seq data

Description

The viewpoint is the bait of 3C method, which can be a promoter region of an interested gene, an enhancer, and a transcrition factor binding region.

Usage

getViewpoint(obj)

Arguments

obj

r3Cseq or r3CseqInBatch object

Value

The viewpoint shows in the IRanges

Author(s)

S. Thongjuea

Examples

#See the vignette

hg18's refGenes

Description

The human (hg18) reference genes from UCSC

hg19's refGenes

Description

The human (hg19) reference genes from UCSC

mm10's refGenes

Description

The mouse (mm10) reference genes from UCSC

mm9's refGenes

Description

The mouse (mm9) reference genes from UCSC

Myb_prom_FB a data set for the example of r3Cseq analysis

Description

The example aligned reads generated by 3C-Seq protocol from fetal brain. The promoter region of the Myb's gene was selected as the viewpoint. This data was transformed from aligned reads shown in the BAM file to GRanged object by using Rsamtools.

Myb_prom_FL a data set for the example of r3Cseq analysis

Description

The example aligned reads generated by 3C-Seq protocol from fetal liver. The promoter region of the Myb's gene was selected as the viewpoint. This data was transformed from aligned reads shown in the BAM file to GRanged object by using Rsamtools.

This method has been removed.

Description

This method has been removed.

Plot domainogram of interaction regions near the viewpoint

Description

Plot domainogram of interaction regions near the viewpoint

Usage

plotDomainogramNearViewpoint(object,smoothing.parameter=0.1,distance=5e5,maximum_window=25e3,view=c("experiment","control","both"))

Arguments

object

r3Cseq or r3CseqInBatch object

smoothing.parameter

A level at which cubic smoothing spline for the spar (see vsmooth.spline) input parameter. Must be in (0.06,0.4] (default=0.1)

distance

Numeric. The distance relative to the viewpoint (default=5e5)

maximum_window

Numeric. The maximum windowing (default=25e3). We normally compute the interaction regions per window starting from 2Kb to maximum window (default=25kb) to make the interaction matrix for visualizing the domainogram.

view

character. The selected view of data (default="experiment")

Value

Plots of domainogram for interaction regions close to the viewpoint

Author(s)

S. Thongjuea

See Also

plotOverviewInteractions, plotInteractionsPerChromosome, plotInteractionsNearViewpoint

Examples

# See the vignette

Plot identified interaction regions near the viewpoint

Description

Plot identified interaction regions near the viewpoint

Usage

plotInteractionsNearViewpoint(obj,distance=5e5,log2fc_cutoff=1,yLim=0)

Arguments

obj

obj is r3Cseq or r3CseqInBatch object

distance

Numeric. The distance relative to the viewpoint (default=5e5)

log2fc_cutoff

Numeric. The log2 cutoff ratio between the experiment and control (default=1)

yLim

Numeric. The limited height of y-axis (default=0)

Value

Plots of identified interaction regions close to the viewpoint

Author(s)

S. Thongjuea

See Also

plotOverviewInteractions, plotInteractionsPerChromosome, plotDomainogramNearViewpoint

Examples

# See the vignette

Plot interaction regions per each chromosome of interest

Description

Plot the distribution of interaction regions per each chromosome

Usage

plotInteractionsPerChromosome(obj, chromosomeName)

Arguments

obj

obj is r3Cseq or r3CseqInBatch object.

chromosomeName

Character. The input chromosome name (e.g. "chr1")

Value

Plots of interaction regions per chromosome.

Author(s)

S. Thongjuea

See Also

plotInteractionsNearViewpoint, plotOverviewInteractions, plotDomainogramNearViewpoint

Examples

# See the vignette

Plot overview of identified interaction regions for genome-wide

Description

Plot the distribution of identified interaction regions across genome

Usage

plotOverviewInteractions(obj, cutoff.qvalue=0.05)

Arguments

obj

obj is r3Cseq or r3CseqInBatch object

cutoff.qvalue

Numeric. The cutoff q-value (default=0.05)

Value

Plots of identified 3C-Seq interaction regions genome-wide

Author(s)

S. Thongjuea

See Also

plotInteractionsNearViewpoint, plotInteractionsPerChromosome, plotDomainogramNearViewpoint

Examples

# See the vignette

r3Cseq objects

Description

The r3Cseq class is the extended class from r3CseqCommon class. It is a general container for storing and manipulating a set of input parameters, RangeData of interactions regions from r3Cseq analysis , and the raw reads GRanged data of the genome-wide interaction signal generated by next-generation sequencing.

Extends

Class r3CseqCommon, directly.

Slots

organismName

Object of class "character" the version of particular assembly genome from UCSC (e.g. mm9, hg18, hg19) . The package supports three genome assemblies consisting of mouse (mm9), and human (hg18, hg19).

restrictionEnzyme

Object of class "character" this is the primary restriction enzyme name using in 3C-Seq experiment

viewpoint_chromosome

Object of class "character" chromosome name of where is the viewpoint located eg. chr10, chrX etc.

viewpoint_primer_forward

Object of class "character" the forward primer DNA sequences for the viewpoint amplification

viewpoint_primer_reverse

Object of class "character" the reverse primer DNA sequences for the viewpoint amplification

expReadCount

Object of class "RangedData" the read count in experiment

contrReadCount

Object of class "RangedData" the read count in control

expRPM

Object of class "RangedData" the normalized read read per million in experiment

contrRPM

Object of class "RangedData" the normalized read read per million in control

expInteractionRegions

Object of class "RangedData" the identified interaction regions in experiment

contrInteractionRegions

Object of class "RangedData" the identified interaction regions in control

isControlInvolved

Object of class "logical" the logical to ask whether the control is involved in the analysis or not

alignedReadsBamExpFile

Object of class "character" the file name of experiment in BAM format

alignedReadsBamContrFile

Object of class "character" the file name of control in BAM format

expLabel

Object of class "character" the experiment name

contrLabel

Object of class "character" the control name

expLibrarySize

Object of class "integer" the library size of experiment

contrLibrarySize

Object of class "integer" the library size of control

expReadLength

Object of class "integer" the read length of experiment

contrReadLength

Object of class "integer" the read length of experiment

expRawData

Object of class "GRanges" the raw reads found in experiment

contrRawData

Object of class "GRanges" the raw reads found in control

Author(s)

S. Thongjuea

See Also

r3CseqCommon, r3CseqInBatch

Examples

# See the vignette

r3CseqCommon objects

Description

The r3CseqCommon class is a general container for storing and manipulating a set of input parameters, RangeData of interactions regions from r3Cseq analysis. It is a root class for r3Cseq and r3CseqInBatch classes.

Slots

organismName

Object of class "character" the version of particular assembly genome from UCSC (e.g. mm9, hg18, hg19) . The package supports three genome assemblies consisting of mouse (mm9), and human (hg18, hg19).

restrictionEnzyme

Object of class "character" this is the primary restriction enzyme name using in 3C-Seq experiment

viewpoint_chromosome

Object of class "character" chromosome name of where is the viewpoint located eg. chr10, chrX etc.

viewpoint_primer_forward

Object of class "character" the forward primer DNA sequences for the viewpoint amplification

viewpoint_primer_reverse

Object of class "character" the reverse primer DNA sequences for the viewpoint amplification

expReadCount

Object of class "RangedData" the read count in experiment

contrReadCount

Object of class "RangedData" the read count in control

expRPM

Object of class "RangedData" the normalized read read per million in experiment

contrRPM

Object of class "RangedData" the normalized read read per million in control

expInteractionRegions

Object of class "RangedData" the identified interaction regions in experiment

contrInteractionRegions

Object of class "RangedData" the identified interaction regions in control

isControlInvolved

Object of class "logical" the logical to ask whether the control is involved in the analysis or not

Author(s)

S. Thongjuea

See Also

r3Cseq, r3CseqInBatch

Examples

# See the vignette

r3CseqInBatch objects

Description

The r3CseqInBatch class is the extended class from r3CseqCommon class. It is a general container for storing and manipulating a set of input parameters, RangeData of interactions regions from r3Cseq analysis for replicates data sets.

Extends

Class r3CseqCommon, directly.

Slots

organismName

Object of class "character" the version of particular assembly genome from UCSC (e.g. mm9, hg18, hg19) . The package supports three genome assemblies consisting of mouse (mm9), and human (hg18, hg19).

restrictionEnzyme

Object of class "character" this is the primary restriction enzyme name using in 3C-Seq experiment

viewpoint_chromosome

Object of class "character" chromosome name of where is the viewpoint located eg. chr10, chrX etc.

viewpoint_primer_forward

Object of class "character" the forward primer DNA sequences for the viewpoint amplification

viewpoint_primer_reverse

Object of class "character" the reverse primer DNA sequences for the viewpoint amplification

expReadCount

Object of class "RangedData" the read count in experiment

contrReadCount

Object of class "RangedData" the read count in control

expRPM

Object of class "RangedData" the normalized read read per million in experiment

contrRPM

Object of class "RangedData" the normalized read read per million in control

expInteractionRegions

Object of class "RangedData" the identified interaction regions in experiment

contrInteractionRegions

Object of class "RangedData" the identified interaction regions in control

isControlInvolved

Object of class "logical" the logical to ask whether the control is involved in the analysis or not

bamFilesDirectory

Object of class "character" the path name of directory that contains BAM files

BamExpFiles

Object of class "vector" the file names of BAM files in the experiment

BamContrFiles

Object of class "vector" the file names of BAM files in the control

expBatchLabel

Object of class "vector" the labeled experiment names

contrBatchLabel

Object of class "vector" the labeled control names

readCountTable

Object of class "RangedData" the read count table

RPMsTable

Object of class "RangedData" the normalized read per million table

expBatchLibrarySize

Object of class "vector" the library size of each experiment

contrBatchLibrarySize

Object of class "vector" the library size of each control

expBatchReadLength

Object of class "vector" the read length of experiments

contrBatchReadLength

Object of class "vector" the read length of controls

Author(s)

S. Thongjuea

See Also

r3CseqCommon, r3CseqInBatch

Examples

# See the vignette

rn5's refGenes

Description

The rat (rn5) reference genes from UCSC