verifyNonExon: Applied to verify if the non-exon sequences are introns.

In VVVVVan/nonexonmap: R Package Template

Description

verifyNonExon use positionNonExon to align the reads with introns and output a BAM file named "verifyNonExonIntrons.BAM". The return value is a data frame with all position of alignment and number of matches and unmatches.

Usage

verifyNonExon(readsFile, referenceFile)

Arguments

readsFile	The file that store the read sequences, a string.
referenceFile	The file that store the reference sequences usually introns, a string.

Value

A data frame contains the name of read, name of reference seqeunces, match/unmatch position and reference start position.

Examples

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

## End(Not run)

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