Data structure for a Hi-C experiment.
An instance of HiCDOCDataSet describes a Hi-C experiment with slots
for path(s) to input file(s), interactions, pipeline parameters defaulting to
defaultHiCDOCParameters, and computation results. It can be
constructed from 4 different types of data:
Tabular files: see HiCDOCDataSetFromTabular
(m)Cool files: see HiCDOCDataSetFromCool
HiC files: see HiCDOCDataSetFromHiC
HiC-Pro matrices and bed files: see HiCDOCDataSetFromHiCPro
An example HiCDOCDataSet is also available, see
exampleHiCDOCDataSet.
inputA vector of path(s) to input file(s).
parametersA list of parameters used for filtering, normalization, and prediction of compartments.
interactionsA tibble of interactions.
chromosomesA vector of names of chromosomes.
conditionsA vector of names of conditions, repeated along the replicates.
replicatesA vector of names of replicates, repeated along the conditions.
positionsA tibble of positions and their corresponding bin.
binSizeThe resolution: computed bin size (span of each bin in number of bases).
totalBinsA list of the number of bins in each chromosome.
weakBinsA list of weak bins that are filtered out in each chromosome.
validConditionsA list of non-sparse valid conditions, repeated along the valid replicates in each chromosome.
validReplicatesA list of non-sparse valid replicates, repeated along the valid conditions in each chromosome.
compartmentsA tibble of the A or B compartment of each bin in each condition.
concordancesA tibble of the concordance of each bin in each replicate.
differencesA tibble of detected compartment differences between conditions.
comparisonsA tibble of comparisons ??? TODO
distancesA tibble of the distances to centroids of each bin in each replicate.
centroidsA tibble of centroids in each chromosome and condition.
selfInteractionRatiosA tibble of differences between self interaction and other interactions for each bin in each replicate.