9 SnipSnip Examples

Using the example data given with the SnipSnip download, perform a basic SnipSnip analysis as follows:

./snipsnip -o results-ExampleData.dat exampleData.bed

In R type:

exampleData<-read.table("K:/code/snipsnip/releases/results-ExampleData.dat", header=T)

plot(exampleData$BP/10^6, -log10(exampleData$P), main="SnipSnip Test",
 xlab=expression(bp~position~(Mb)), ylab=expression(-log[10](p-value)), ylim=c(0,15)) 
abline(h=8, lty=2)

This will produce the following plot:

Figure 3. Manhattan plot of SnipSnip test results.

To also perform standard logistic regression use the -lr option as follows:

./snipsnip -lr -o results-ExampleData-LR.dat exampleData.bed

To plot the standard logistic regression test results type:

exampleDataLR<-read.table("K:/code/snipsnip/releases/results-ExampleData-LR.dat", header=T)

plot(exampleDataLR$BP/10^6, -log10(exampleDataLR$P_LR), main="Standard Logistic Regression",
 xlab=expression(bp~position~(Mb)), ylab=expression(-log[10](p-value)), ylim=c(0,15)) 
abline(h=8, lty=2)

This will produce the following plot:

Figure 4. Manhattan plot of standard logistic regression test results.