countReads: Count and summarize long-reads RNA into a table

In leetina4/LSplicing: Generates Long-reads Splicing Graph

Description

A function that ouputs two tsv files containing counts of exon combinations

Usage

countReads(alnsFile, referencesFile)

Arguments

alnsFile	The file that store the long-read RNA alignments generated by Minimap2.
referencesFile	A file that store reference coordinates of human genes.

Value

A list of two data frames. Fisrt data frame contains new exon coordinates created and second data frame contains the exon combinations of each read.

Examples

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

## Not run: 
countReads(alns = alignments, refCoord = referenceCoord)

## End(Not run)

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