FiRePat processing parameters

The user can specify the following processing parameters. All these parameters have preset default values which are used if the user does not change them.

• Whether sRNA data should be filtered, the default is yes.
• The percentage of sRNA sequences for which data should be retained when filtering, the default is10%.
• Whether non-sRNA data should be filtered, the default is yes.
• The minimum expression level for non-sRNA data to be retained, the default is 10.
• Which correlation method should be used: Kendall, Pearson or Spearman. The default method is Pearson.
• Whether local correlations should be used, the default is no.
• The minimum window width to use for local correlations. The lowest and default value is 4. If less than 4 is entered, the value will be reset to 4.
• Absolute correlation threshold value. The value below which a pair of sequences will not be retained. The default is 0.9, i.e. sequence pairs will only be retained if their correlation is 0.9 or greater, or -0.9 or less.