mainNonexonmap: An main function to plot the non-exon on reference gene.

In VVVVVan/nonexonmap: R Package Template

Description

mainNonExonMap This is the main function for my functions in this package. The function will plot the non-exon position on reference gene and if they are introns (if intronsFile exist).

Usage

mainNonExonMap(readsFile, transcriptsFile, intronsFile = "")

Arguments

readsFile	The file that store the read sequences, a string.
transcriptsFile	The file that store the reference sequences, a string.
intronsFile	The file that contains the intron sequences, a string.

Value

A list of list with reference name, alignment position, alignment counts and percentage of introns if there is a verifyDataFrame.

Examples

readsFile <- system.file("extdata/testdata", "RRHreads.fasta", package = "nonexonmap")
transcriptsFile <- system.file("extdata/testdata", "RRHtranscript.fasta", package = "nonexonmap")
intronsFile <- system.file("extdata/testdata", "RRHintrons.fasta", package = "nonexonmap")
## Not run: 
mainNonExonMap(readsFile, transcriptsFile)
mainNonExonMap(readsFile, transcriptsFile, intronsFile)

## End(Not run)

VVVVVan/nonexonmap documentation built on May 30, 2019, 11:48 p.m.