Download User Guide for nagnag Package

## produce RNA sequence
n.df <- nagnagSeq(nagEvent, genomeFasta, gtfFile, type="RNA")
## produce amino acid sequences
n.df <- nagnagSeq(nagEvent, genomeFasta, gtfFile, type="AA")
Use ?
3.4
3.4.1
combineCount for details about parameters.
Summarize the results
nagnagSum
altRef <- altSearch(gtfFile, AStype="acceptor", transcriptNameStyle="arab")
nagnagSum(altRef)
nagRef <- nagnagDetect(altRef, genomeFasta)
nagnagSum(nagRef)
nag.expr <- nagnagExpr(bamFile, genomeFasta, nagRef=NULL)
nagnagSum(nag.expr)
This function provides summary for the results from altSearch, nagnagDetect
and nagnagExpr function.
3.5
3.5.1
Visualize the results
nagnagVis
altRef <- altSearch(gtfFile, AStype="acceptor", transcriptNameStyle="arab")
jpeg(file="test.jpg")
nagnagVis(altRef)
dev.off()
nagRef <- nagnagDetect(altRef, genomeFasta)
jpeg(file="test.jpg")
nagnagVis(nagRef)
dev.off()
nag.expr <- nagnagExpr(bamFile, genomeFasta, nagRef=NULL)
jpeg(file="test.jpg")
nagnagVis(nag.expr)
dev.off()
This function provides visualization for the results from altSearch, nagnagDetect
and nagnagExpr function. It generates figure files as PDF, jpeg, tiff, etc.
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Demonstration
1. RNA-Seq data for Arabidopsis.
Example data is available at http://genome.sdau.edu.cn/research/software/nagnag.html.
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