LONGO is designed to have two different uses. One through a shiny interface and another through R. Both of results of the program are the same. The shiny interface will allow the user to alter certain variables in the analysis to see how they will affect the result. This can be useful when interpreting new data.
LONGO is designed to take in a data file with a gene identifier to get the gene name and length. Occasionally there will be multiple probes going to a single gene. LONGO can handle this in two different ways. The default way is to get the mean expression values. The other option is to only keep the probe that has the highest overall expression values. If a read has no identified gene name or length in BioMart, the read is removed.
After getting the gene names and lengths the data is sorted by length. A rolling window is used to create bins. The user can change the size of the window as well as the step size of the window. These rolling window values are then plotted. The P value plot shows the p value comparisons of the values making up the windows to the window values in the control.