fitevd

Usage:

fitevd <query length> [options]

Description

fitevd fits an extreme value distribution to a set of score-length pairs.

The outer loop alternates between estimating lambda and K with H fixed and estimating H with lambda and K fixed. The inner loop is the Newton-Raphson algorithm, which is used for solving the estimation problems.

Input

Reads white-space separated score-length pairs from standard input.

Query Length

The query length; ignored for -exp and -gcexp.

Output

Writes the EVD parameters to standard output.

Options

Option Parameter Description Default Behavior
General Options
-exp Compute an exponential-Guassian mixture. Compute EVD.
-gcexp Compute a GC-dependent exponential-Guassian mixture. Compute EVD.
-ss Size of length groups. The size of length groups is 10,000.
-msms Minimum number of scores per length (or GC-content) group. Note: If ms is 0 and -gcexp is given, then no binning is done and weighted regression is used. The size of length groups is 200.
-lrlr Minimum ratio of shortest to longest in group. The minimum ratio of shortest to longest in the group is 1.50.
-rn Use n randomly selected scores. All are used.
-p  Print p-values. The p-values are not printed.
-hH Initial value of H. H is set to 1.0.
-ilhilh Maximum iterations in outer L-H loop. The maximum iterations in outer L-H loop is 10.
-inrinr Maximum iterations in inner N-R loop. The maximum iterations in inner N-R loop is 20.
-dsmin smax Print length vs p-value for smin ≤ score ≤ smax. Do not print length vs. p-value.
-t  Turn on debug tracing. Debug tracing is not on.