ConsensusPeaks: Find Consensus Peaks

In neurogenomics/CHAS: Cell type deconvolution of bulk tissue histone acetylomes from epigenetic data

Find Consensus Peaks

Description

This function identifies the consensus peaks and their counts in each bulk and reference samples by switching IDs

Usage

ConsensusPeaks(bulkPeaks, bulkCounts, refPeaks, refCounts)

Arguments

bulkPeaks	A data frame of bulk H3K27ac peaks in BED format the first column contains the chromosome number following 'chr', such as 'chr1' the second column contains the start position of the peak the third column contains the end position of the peak the fourth column contains the peak identifier
bulkCounts	A counts matrix for bulk data rows represent peaks, using the same identifier as bulkPeaks columns represent bulk samples
refPeaks	A data frame of reference H3K27ac peaks in BED format the first column contains the chromosome number, such as 'chr1' the second column contains the start position of the peak the third column contains the end position of the peak the fourth column contains the peak identifier
refCounts	A counts matrix for reference data the rows represent peaks, using the same identifier as refPeaks the columns represent cell-type samples, and can have one or multiple samples for each cell type

Details

This function takes four inputs: bulk: peak location, raw counts reference: peak location, raw counts

This function has three steps: (1) find consensus peaks in bulk and reference (2) assign new identifiers to consensus peaks (3) filter the counts matrices to contain only the consensus peaks

Value

A list containing the following: 1 data frame: bulk counts for consensus peaks 2 data frame: reference counts for consensus peaks

neurogenomics/CHAS documentation built on Jan. 20, 2025, 4:03 p.m.