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

Description Usage Arguments Details Value See Also

View source: R/coverage_cal_functions.R

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

1
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 May 25, 2021, 12:40 a.m.