readCoverage: Calculates coverage of long-reads RNA

In leetina4/LSplicing: Generates Long-reads Splicing Graph

Description

A function that calculates the coverage of long-read RNA

Usage

readCoverage(coor, alns)

Arguments

coor	A data frame containing exon coordinates of target gene.
alns	A GAlignment object of long-read RNA alignments generated by Minimap2.

Value

A data frame that stores the coverage of the reads

Examples

alignments <- system.file("extdata", "mlx_reads.sorted.bam",
package = "LSplicing")
referenceCoord <- system.file("extdata", "example_refCoord.gff3",
package = "LSplicing")

## Not run: 
results <- countReads(alignments, referenceCoord)
coor <- results[[1]]
coor <- coor[coor$gene_id == "ENSG00000108788.11", ]
readCoverage(coor = coor,
             alns = alignments)

## End(Not run)

leetina4/LSplicing documentation built on Dec. 8, 2019, 1:34 p.m.