NucDyn-class: Nucleosome Dynamics calculation.
In nucleosome-dynamics/NucDyn: Nucleosome Dynamics

Description Details Value Slots Author(s) See Also

This class represents the result of running nucleosomeDynamics on two reference sets.

Intances of this class contain two GRangesList objects, each with information about how reads were classified in each input dataset. The fields of each GRangesList object are (with some exceptions*):

originals: All reads used for the analysis, after removing long reads defined by maxLen parameter.
coinciding: Reads that have an exact match in the other set and are considered to be the same read.
same.start: Reads whose match in the other set starts at the same position but ends in a different one. They are considered to be a consequence of experimental differences.
same.end: Reads whose match in the other set ends at the same position but starts in a different one. They are considered to be a consequence of experimental differences.
containedA: Reads in the set B which are totally contained by their match in the set A. Or reads in the set A that totally contain their match in the set B. They are considered to be a consequence of experimental differences.
containedB: Reads in the set A which are totally contained by their match in the set B. Or reads in the set B that totally contain their match in the set A. They are considered to be a consequence of experimental differences.
small.shifts: Upstream or downstream shifts shorter than minDiff.
left.shifts: Shifts that suffer an upstream shift when considering transition from the set A to the set B.
right.shifts: Shifts that suffer a downstream shift when considering transition from the set A to the set B.
indels: Reads that are not present in the other set due to an insertion or deletion event. If they are in set A, they are considered a deletion and if they are in set B, they are considered an insertion.
unpaired: Reads that are uniformly and randomly removed from the set with more reads to account for differences in the number of reads between sets.