| compute_consensus_peaks | R Documentation |
Compute consensus peaks
Description
Compute consensus peaks from a list of GRanges.
Usage
compute_consensus_peaks(
grlist,
groups = NULL,
genome_build,
lower = 2,
upper = Inf,
min.gapwidth = 1L,
method = c("granges", "consensusseeker"),
...
)
Arguments
grlist |
Named list of GRanges objects.
|
groups |
A character vector of the same length as grlist
defining how to group GRanges objects when
computing consensus peaks.
|
genome_build |
Genome build name.
|
lower, upper |
The lower and upper bounds for the slice.
|
min.gapwidth |
Ranges separated by a gap of at least min.gapwidth positions
are not merged.
|
method |
Method to call peaks with:
|
... |
Arguments passed on to consensusSeekeR::findConsensusPeakRegions
narrowPeaksa GRanges containing
called peak regions of signal enrichment based on pooled, normalized data
for all analyzed experiments. All GRanges entries must
have a metadata field called "name" which identifies the region to
the called peak. All GRanges entries must also
have a row name which identifies the experiment of origin. Each
peaks entry must have an associated narrowPeaks entry.
A GRanges entry is associated to a narrowPeaks entry by
having a identical metadata "name" field and a identical row name.
peaksa GRanges containing called peaks of signal
enrichment based on pooled, normalized data
for all analyzed experiments. All GRanges entries must
have a metadata field called "name" which identifies the called
peak. All GRanges entries must
have a row name which identifies the experiment of origin. Each
peaks entry must have an associated narrowPeaks entry. A
GRanges entry is associated to a narrowPeaks entry by having
a identical metadata "name" field and a identical row name.
chrInfoa Seqinfo containing the name and the length of the
chromosomes to analyze. Only the chomosomes contained in this
Seqinfo will be analyzed.
extendingSizea numeric value indicating the size of padding
on both sides of the position of the peaks median to create the
consensus region. The minimum size of the consensus region is
equal to twice the value of the extendingSize parameter.
The size of the extendingSize must be a positive integer.
Default = 250.
expandToFitPeakRegiona logical indicating if the region size,
which is set by the extendingSize parameter is extended to include
the entire narrow peak regions of all peaks included in the unextended
consensus region. The narrow peak regions of the peaks added because of the
extension are not considered for the extension. Default: FALSE.
shrinkToFitPeakRegiona logical indicating if the region size,
which is set by the extendingSize parameter is shrinked to
fit the narrow peak regions of the peaks when all those regions
are smaller than the consensus region. Default: FALSE.
minNbrExpa positive numeric or a positive integer
indicating the minimum number of experiments in which at least one peak
must be present for a potential consensus region. The numeric must be a
positive integer inferior or equal to the number of experiments present
in the narrowPeaks and peaks parameters. Default = 1.
nbrThreadsa numeric or a integer indicating the
number of threads to use in parallel. The nbrThreads must be a
positive integer. Default = 1.
|
Details
NOTE: If you get the error
"Error in serialize(data, node$con) : error writing to connection",
try running closeAllConnections
and rerun compute_consensus_peaks.
This error can sometimes occur when
compute_consensus_peaks
has been disrupted partway through.
Value
Named list of consensus peak GRanges.
Source
GenomicRanges tutorial
consensusSeekeR
Examples
data("encode_H3K27ac") # example dataset as GRanges object
data("CnT_H3K27ac") # example dataset as GRanges object
data("CnR_H3K27ac") # example dataset as GRanges object
grlist <- list(CnR=CnR_H3K27ac, CnT=CnT_H3K27ac, ENCODE=encode_H3K27ac)
consensus_peaks <- compute_consensus_peaks(grlist = grlist,
groups = c("Imperial",
"Imperial",
"ENCODE"))
