# GlossaryΒΆ

- Interval
- a (genomic) segment with a chromosomal location (contig,start and end).
- Intervals
- a set of one or more intervals.
- workspace
- the genomic regions accessible for simulation.
- annotations
- sets of intervals annotating various regions of the genome.
- segments of interest
- sets of intervals whose association is tested with annotations
- sampled segments
- randomized versions of the segments of interest. A set of sampled segments is one sample.
- sample
- one set of sampled segments.
- isochore
- Usually, isochores are defined as genomic regions of homogeneous G+C content. In GAT, isochores can mean any genomic regions with a shared property. Isochores are used to eliminate the effect of confounders in an analysis.
- isochores
- plural of isochore.
- isochore workspaces
- the workspace split according to isochores.
- bed
- an interval format. Intervals are in a tab-separated list denoted
as
`contig`

,`start`

,`end`

. A bed file can contain several tracks which will be treated independently. Tracks are either delineated by a line of the format:`track name=<trackname>`

or by an optional fourth column (field`name`

). See UCSC for more information about bed files. - fold
- fold change, computed as the ratio of observed over expected
- p-value
- significance of association. The P-value is an estimate of the probability to obtain an observed (or larger) overlap between two segment sets by chance.
- q-value
- multiple testing corrected p-value. The qvalue can either be
computed using the q-value procedure suggested by
Storey et al. (2002) or using other FDR approaches
such as Bonferroni, Benjamini-Hochberg, etc. implemented
in the R function
`p.adjust`

. - pvalue
- the column containing the p-value.
- qvalue
- the column containing the q-value.
- track
- a set of segments within a bed formatted file. Tracks
are either grouped using the
`track name=<trackname>`

prefix or by an optional fourth column (the`name`

column). - annotation
- a genomic annotation, which is a collection of intervals.
- observed
- the observed value of a metric.
- expected
- the expected value of a metric as determined by simulations.
- fold
- the fold change, defined as the ratio of observed over expected.
- l2fold
- the logarithm (base 2) of fold change.
- tracks
- plural of track
- samples
- a set of samples (see sample)