- a (genomic) segment with a chromosomal location (contig,start and end).
- a set of one or more intervals.
- the genomic regions accessible for simulation.
- 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.
- one set of sampled segments.
- 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.
- plural of isochore.
- isochore workspaces
- the workspace split according to isochores.
- an interval format. Intervals are in a tab-separated list denoted
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 change, computed as the ratio of observed over expected
- 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.
- 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
- the column containing the p-value.
- the column containing the q-value.
- 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
- a genomic annotation, which is a collection of intervals.
- the observed value of a metric.
- the expected value of a metric as determined by simulations.
- the fold change, defined as the ratio of observed over expected.
- the logarithm (base 2) of fold change.
- plural of track
- a set of samples (see sample)