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)