plotReads: plotReads.R

In leetina4/LSplicing: Generates Long-reads Splicing Graph

Description

A function that plots results exon combination of target gene (plots results of countReads function).

Usage

plotReads(coor, reads, gene, alnsFile)

Arguments

coor	A data frame that contains exon coordinates of different genes.
reads	A data frame containing rows of reads. If a value = 1, then that row of read is mapped to that column of exon. If a value = 0, then that row of read is not mapped to that column of exon.
gene	A string of characters representing Ensembl gene ID of the gene of interest.
alnsFile	The file that store the long-read RNA alignments generated by Minimap2.

Value

A ggplot graph that represent the long-read RNAs exon combinations

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]]
r <- results[[2]]
plotReads(coor = coor,
          reads = r,
          gene = "ENSG00000108788.11",
          alns = alignments)

## End(Not run)

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