# Phaser

## About Phaser

### What does Phaser do?

Given a set of loci and diurnal or circadian time course, Phaser determines which of those loci are rhythmic and then which (if any) phases of the peak expression are overrepresented in the sample. It does this by assuming that the sampled loci are taken at random from the genome and then compares the actual counts for each phase against what would be expected according to the background.

The p-values are calculated using binomial random variables for each phase bin. Namely, the background probability that a randomly selected locus belongs to a particular phase is calculated and then used to calculate the binomial distribution for that phase bin. The observed phase bin count as determined in the input locus set is then used to calculate a p-value from the corresponding binomial distribution.

Previously, Phaser worked by using the normal approximation to the binomial distribution. For large query sets, the differences between the two are negligible. However, since the binomial distribution is exact, Phaser's results can be better trusted for smaller query sets.

### What does the correlation cutoff do?

Not every locus has a rhythmic expression pattern under a given condition. In fact, the notion of rhythmicity is not completely objective, because some patterns exhibit more rhythmicity than others. The correlation cutoff allows the user to control what is considered rhythmic and what is not. Namely, for those familiar with Diurnal, every gene expression pattern is fitted with a best-fit model. Each of these fits has a corresponding correlation that describes the overall quality of the fit. Any fit above the correlation cutoff will be considered rhythmic with the phase of the best-fit model. Anything else is treated as non-rhythmic.

### How can I download the unfiltered results for all of the words?

This can be done by using the fixed cutoff filter and choosing a cutoff of 1, meaning that nothing will be filtered out. You will then be able to download the results using the link on the job page.

### What do all of the conditions mean?

Please see Diurnal for details.