loadBpCoverages: Load a BAM file and calculate coverages of each position with...

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Load a BAM file and calculate coverages of each position with derfinder

Description

Load a BAM file and calculate coverages of each position with derfinder

Usage

loadBpCoverages(files, chrs, ...)

Arguments

files	BAM files which need the corresponding index files (.bai).
chrs	Chromosome information.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'.

Value

A list with one element per chromosome. Each element is a DataFrame with the coverage information.

Examples

## Not run: 
chrs <- c(as.character(1:19),'X','Y')
fullcovF <- loadBpCoverages('./dedup_h2.forward.sorted.bam', chrs)

## End(Not run)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.