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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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inst/reports/runReport.Rmd
 
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Run Report
 
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==========
 
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Run Parameters
 
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-------------------
 
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```{r}
 
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alpha=0.05
 
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runInfo()
 
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```
 
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Global Statistics
 
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-----------------
 
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```{r}
 
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cuff
 
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```
 
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### FPKM distributions
 
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```{r fig.width=7, fig.height=6}
 
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csDensity(genes(cuff))
 
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csDensity(isoforms(cuff))
 
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```
 
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### Scatterplots
 
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```{r}
 
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csScatterMatrix(genes(cuff),logMode=T)
 
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```
 
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Replicate Information
 
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---------------------
 
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Model fit
 
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---------
 
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Differential Expression Analysis
 
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--------------------------------
 
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### Significant Genes
 
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```{r fig.width=6,fit.height=6}
 
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sigMatrix(cuff,level="genes")
 
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```
 
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```{r}
 
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csVolcanoMatrix(genes(cuff),alpha=alpha)
 
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```
 
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```{r}
 
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sigGeneIDs<-getSig(cuff,alpha=alpha)
 
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sigGenes<-getGenes(cuff,sigGeneIDs)
 
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```
 
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There are `r length(sigGeneIDs)` significantly different genes at a `r alpha*100`$\%$ FDR. 
 
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#### Visualizations
 
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```{r fig.width=6,fit.height=10}
 
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csHeatmap(sigGenes,cluster="both",labRow=F)
 
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```
 
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### Significant Isoforms
 
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```{r fig.width=6,fit.height=6}
 
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sigMatrix(cuff,level="isoforms")
 
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```
 
 
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