MmapprData-class: MmapprData Class

Description Slots See Also

Description

Stores data from each step of the MMAPPR2 pipeline.

Slots

param

MmapprParam object storing parameters used in analysis.

distance

List containing raw counts and Euclidean distance data for each chromosome. After calculateDistance, chromosomes with sufficient data should have $wtCounts, $mutCounts, and $distanceDf populated. After loessFit, the $distanceDf element for each chromosome list is replaced with a $loess element.

peaks

List of chromosomes containing peak regions. Initialized after prePeak and populated with density function after peakRefinement.

candidates

List containing GRanges object for each peak, resulting from generateCandidates function. VEP data, including gene symbol and consequence for each variant, are included in metacolumns.

See Also

mmappr, MmapprData-getters


kjohnsen/MMAPPR2 documentation built on Oct. 1, 2019, 7:01 p.m.