calcSummarySignal: The function calcSummarySignal takes the input BED file(s) in...
In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor
View source: R/specificity-plots.R
calcSummarySignal R Documentation
The function calcSummarySignal takes the input BED file(s)
in form of GRanges or GRangesList object, overlaps
it with all defined open chromatin regions across
conditions (e.g. cell types) and returns a matrix,
where each row is the input genomic region
(if overlap was found), each column is a condition,
and the value is a meam signal from regions where
overlap was found.
Description
The function calcSummarySignal takes the input BED file(s)
in form of GRanges or GRangesList object, overlaps
it with all defined open chromatin regions across
conditions (e.g. cell types) and returns a matrix,
where each row is the input genomic region
(if overlap was found), each column is a condition,
and the value is a meam signal from regions where
overlap was found.
Usage
calcSummarySignal(query, signalMatrix)
Arguments
query
Genomic regions to be analyzed. Can be GRanges or GRangesList
object.
signalMatrix
Matrix with signal values in predfined regions, where
rows are predefined genomic regions, columns are conditions
(e.g. cell types in which the signal was measured).
First column contains information about the genomic region in
following form: chr_start_end.
Can be either data.frame or data.table object.
Value
A list with named components:
signalSummaryMatrix - data.table with cell specific open chromatin signal
values for query regions
matrixStats - data.frame containing boxplot stats for individual
cell type
Examples
signalSummaryList = calcSummarySignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)
databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.
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View source: R/specificity-plots.R
| calcSummarySignal | R Documentation |
The function calcSummarySignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across conditions (e.g. cell types) and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a condition, and the value is a meam signal from regions where overlap was found.
Description
The function calcSummarySignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across conditions (e.g. cell types) and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a condition, and the value is a meam signal from regions where overlap was found.
Usage
calcSummarySignal(query, signalMatrix)
Arguments
query |
Genomic regions to be analyzed. Can be GRanges or GRangesList object. |
signalMatrix |
Matrix with signal values in predfined regions, where rows are predefined genomic regions, columns are conditions (e.g. cell types in which the signal was measured). First column contains information about the genomic region in following form: chr_start_end. Can be either data.frame or data.table object. |
Value
A list with named components: signalSummaryMatrix - data.table with cell specific open chromatin signal values for query regions matrixStats - data.frame containing boxplot stats for individual cell type
Examples
signalSummaryList = calcSummarySignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)
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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