countNonExon: Count the numbers, the position, percentage of introns for...

In VVVVVan/nonexonmap: R Package Template

Description

countNonExon is a function that is used to count the number of non- exon sequences on specific position of reference sequences and output the percentage of introns in those non-exon sequences.

Usage

countNonExon(findDataFrame, verifyDataFrame = data.frame())

Arguments

findDataFrame	the data frame that store the information for funciton to analyze. Should compute from findNonExon or relateive functions.
verifyDataFrame	the data frame that store the information for funciton to analyze. Should compute from verifyNonExon or relateive functions.

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: 
finddataframe <- findNonExon(readsFile, transcriptsFile)
countNonExon(finddataframe)
verifydataframe <- verifyNonExon(readsFile, intronsFile)
countNonExon(finddataframe, verifydataframe)

## End(Not run)

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