CelltypeSpecificPeaks: Identify cell type-specific peaks in bulk tissue H3K27ac...
In neurogenomics/CHAS: Cell type deconvolution of bulk tissue histone acetylomes from epigenetic data
View source: R/CelltypeSpecificPeaks.R
CelltypeSpecificPeaks R Documentation
Identify cell type-specific peaks in bulk tissue H3K27ac profiles
Description
This function takes as input bulk H3K27ac peaks and cell type sorted H3K27ac peaks,
and will generate a data frame with annotated bulk peaks and another data frame
made up of the cell type specific bulk peaks.
Usage
CelltypeSpecificPeaks(bulkPeaks, celltypePeaks, p)
Arguments
bulkPeaks
A data frame of bulk H3K27ac peaks in BED format, with the first
column containing the chromosome number, the second column containing the start
position of the peak, the third column containing the end position of the peak, and
the fourth column containing the peak identifier.
celltypePeaks
A data frame of celltype H3K27ac peaks in BED format, with the
first column containing the chromosome number, the second column containing the start
position of the peak, the third column containing the end position of the peak, and
the fourth column containing the peak identifier.
p
A number from 0-1 determining the percentage overlap required for a bulk peak
to be considered cell type specific.
Value
A data frame of annotated bulk peaks and a data frame containing only the cell type
specific bulk peaks.
neurogenomics/CHAS documentation built on Jan. 20, 2025, 4:03 p.m.
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View source: R/CelltypeSpecificPeaks.R
| CelltypeSpecificPeaks | R Documentation |
Identify cell type-specific peaks in bulk tissue H3K27ac profiles
Description
This function takes as input bulk H3K27ac peaks and cell type sorted H3K27ac peaks, and will generate a data frame with annotated bulk peaks and another data frame made up of the cell type specific bulk peaks.
Usage
CelltypeSpecificPeaks(bulkPeaks, celltypePeaks, p)
Arguments
bulkPeaks |
A data frame of bulk H3K27ac peaks in BED format, with the first column containing the chromosome number, the second column containing the start position of the peak, the third column containing the end position of the peak, and the fourth column containing the peak identifier. |
celltypePeaks |
A data frame of celltype H3K27ac peaks in BED format, with the first column containing the chromosome number, the second column containing the start position of the peak, the third column containing the end position of the peak, and the fourth column containing the peak identifier. |
p |
A number from 0-1 determining the percentage overlap required for a bulk peak to be considered cell type specific. |
Value
A data frame of annotated bulk peaks and a data frame containing only the cell type specific bulk peaks.
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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