ReadCounting: Read Counting

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

Read Counting

Description

This function counts the reads in bulk and reference bam files ar the union peaks.

Usage

ReadCounting(unionPeaksSaf, bulkDir, refDir, threads = 8, PairedEnd = FALSE)

Arguments

unionPeaksSaf	Path to the SAF file containing the union peaks.
bulkDir	Directory path where all the bulk BAM files are located. The name of the input BAM files must only contain the sample ID, such as 'SRR5927824.bam' for the bulk sample 'SRR5927824'
refDir	Directory path where all the reference BAM files are located. The name of the input BAM files must only contain the sample ID, such as 'astrocyte_1.bam' for the reference sample 'astrocyte_1'.
threads	The number of threads for running featureCounts. The default is 8.

Details

This function takes three main inputs: the directory to where the bulk and reference bam files are stored, and the directory to the .saf file.

Value

A list containing two dataframes the first data frame contains the bulk counts the second data frame contains the reference counts

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