read_coverage: Function to calculate read coverage score for one bam file
In DegNorm: DegNorm: degradation normalization for RNA-seq data

Description Usage Arguments Details Value See Also

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.

1	read_coverage(bam_file,all_genes,cores)

`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.

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.

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

read_coverage_batch

DegNorm documentation built on Nov. 8, 2020, 7:34 p.m.