read_coverage: Function to calculate read coverage score for one bam file

In jipingw/DegNorm: DegNorm: degradation normalization for RNA-seq data

Function to calculate read coverage score for one bam file

Description

This function judges whether bam file is single-end and paired-end, and generate bam file index if needed. It calls function paired_end_cov_by_ch or single_end_by_ch. It takes multiple-core structure for parallel computing for efficiency.

Usage

read_coverage(bam_file,all_genes,cores)

Arguments

bam_file	The name of the bam file.
all_genes	An GRangesList object. It's the parsed genes annotation file from GTF file.
cores	number of cores to use.

Details

This function judges whether bam file is single-end and paired-end, and generate bam file index if needed. It takes multiple-core structure for parallel computing for efficiency.

Value

This function returns a coverageClass object. It contains a list of: (1) a list of coverage score for each gene in RLE format and (2) a dataframe for read counts

See Also

read_coverage_batch

jipingw/DegNorm documentation built on April 3, 2024, 1:22 a.m.