positionNonExon: Output the positions of reads on reference sequences with...

In VVVVVan/nonexonmap: R Package Template

Description

positionNonExon uses buildindex and align to form an alignment file. From the file, output the position of non-exon sequences exist on the references sequences and the match/unmatch numbers in the reads itself.

Usage

positionNonExon(readsFile, referencesFile, outputsFile)

Arguments

readsFile	The file that store the read sequences, a string.
referencesFile	The file that store the reference sequences, a string.
outputsFile	The name of output file in BAM format, a string.

Value

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

See Also

buildindex Build an index for read mapping to perform.

align Align DNA and RNA sequencing reads and report.

scanBam Read the Bam file.

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: 
positionNonExon(readsFile, transcriptsFile, "outputReadsTranscript.BAM")
positionNonExon(readsFile, intronsFile, "outputReadsIntron.BAM")

## End(Not run)

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