aggregate_nearby_peaks: Make an aggregate count cds by collapsing nearby peaks
In cole-trapnell-lab/cicero-release: Predict cis-co-accessibility from single-cell chromatin accessibility data
aggregate_nearby_peaks R Documentation
Make an aggregate count cds by collapsing nearby peaks
Description
Make an aggregate count cds by collapsing nearby peaks
Usage
aggregate_nearby_peaks(cds, distance = 1000)
Arguments
cds
A CellDataSet (CDS) object. For example, output of
make_atac_cds
distance
The distance within which peaks should be collapsed
Details
This function takes an input CDS object and collapses features
within a given distance by summing the values for the collapsed features.
Ranges of features are determined by their feature name, so the feature
names must be in the form "chr1:1039013-2309023".
Value
A CDS object with aggregated peaks.
Examples
data("cicero_data")
input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
agg_cds <- aggregate_nearby_peaks(input_cds, distance = 10000)
cole-trapnell-lab/cicero-release documentation built on Sept. 4, 2024, 1:49 p.m.
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| aggregate_nearby_peaks | R Documentation |
Make an aggregate count cds by collapsing nearby peaks
Description
Make an aggregate count cds by collapsing nearby peaks
Usage
aggregate_nearby_peaks(cds, distance = 1000)
Arguments
cds |
A CellDataSet (CDS) object. For example, output of
|
distance |
The distance within which peaks should be collapsed |
Details
This function takes an input CDS object and collapses features within a given distance by summing the values for the collapsed features. Ranges of features are determined by their feature name, so the feature names must be in the form "chr1:1039013-2309023".
Value
A CDS object with aggregated peaks.
Examples
data("cicero_data")
input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
agg_cds <- aggregate_nearby_peaks(input_cds, distance = 10000)
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.
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