findNonExon: Applied to find the non-exon sequences in reads.

In VVVVVan/nonexonmap: R Package Template

Description

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

Usage

findNonExon(readsFile, referencesFile)

Arguments

readsFile	The file that store the read sequences, a string.
referencesFile	The file that store the reference sequences usually transcripts, 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")
transcriptsFile <- system.file("extdata/testdata", "RRHtranscript.fasta", package = "nonexonmap")
## Not run: 
dataFrame <- findNonExon(readsFile, transcriptsFile)

## End(Not run)

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