Add default values of some parameters to the help file.
<ul>
<li><b>Min confidence</b> (number between 0 and 1) is a fraction of the total number of samples. An aligned compound
must be detected at least in several samples. This parameter determines the minimum number of samples where a
- compound must be detected.
+ compound must be detected. The default value is 0.7, so an aligned compound must be observed at least in 70% of
+ all samples.
</li>
<li><b>Retention time range</b> (minutes) is the maximum allowed retention time difference between aligned compounds
equal.</li>
<li><b>Score threshold</b> (number between 0 and 1) is the minimum value of the similarity function S(C<sub>1</sub>,
- C<sub>2</sub>) required for compounds to be aligned together.
+ C<sub>2</sub>) required for compounds to be aligned together. The default value is 0.75.
</li>
<li><b>Score weight</b> (number between 0 and 1) is the weight w that is used in the similarity function
- S(C<sub>1</sub>, C<sub>2</sub>).
+ S(C<sub>1</sub>, C<sub>2</sub>). The default value is 0.1.
</li>
<li><b>Retention time similarity</b> chooses a method used for calculating the retention time similarity.
