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
.
input
A vector of path(s) to input file(s).
parameters
A list of parameters used for filtering, normalization, and prediction of compartments.
interactions
A tibble of interactions.
chromosomes
A vector of names of chromosomes.
conditions
A vector of names of conditions, repeated along the replicates.
replicates
A vector of names of replicates, repeated along the conditions.
positions
A tibble of positions and their corresponding bin.
binSize
The resolution: computed bin size (span of each bin in number of bases).
totalBins
A list of the number of bins in each chromosome.
weakBins
A list of weak bins that are filtered out in each chromosome.
validConditions
A list of non-sparse valid conditions, repeated along the valid replicates in each chromosome.
validReplicates
A list of non-sparse valid replicates, repeated along the valid conditions in each chromosome.
compartments
A tibble of the A or B compartment of each bin in each condition.
concordances
A tibble of the concordance of each bin in each replicate.
differences
A tibble of detected compartment differences between conditions.
comparisons
A tibble of comparisons ??? TODO
distances
A tibble of the distances to centroids of each bin in each replicate.
centroids
A tibble of centroids in each chromosome and condition.
selfInteractionRatios
A tibble of differences between self interaction and other interactions for each bin in each replicate.