Description Usage Arguments Details Value Author(s) References See Also
A function to test for spatial inconsistencies in a calibrated Hi-C distance matrix.
1 |
calibHiC |
A M*M Hi-C matrix,providing pairwise calibrated distances between M genomic bins. Zero off-diagonal values represent discarded/missing information. This matrix could be prepared with the function |
hicCoord |
The genomic coordinates of the M Hi-C bins. A data frame with the following mandatory columns: chr (chromosome name), start (start position), end (end position). Additional columns are permitted but will not be used. |
Denote delta(i,j) the calibrated Hi-C distances, then delta(i,j) define a weighted undirected graph G{V, E}, where V is the set of loci (bins) and E is the set of edges: {(vi,vj)| delta(i,j) > 0, i != j} with weights delta(i,j). We distinguish here between immediate neighbors from the same chromosome (cis) and from different chromosomes (trans) and detect a spatial inconsistency for a node v in G, if the sub-graph G' of all (immediate) trans neighbors of v is not connected. Further identifying the connected components in G' can highlight the cause of inconsistency and the underlying spatial division.
A list with the following values:
neighborhoods |
A list of length M, where neighborhoods[i] gives the neighborhood of i, if a spatial inconsistency was detected for i, and NULL otherwise. Here, the neighborhood of i is the sub-graph of immediate neighbors in trans, an |
indices |
The indices of loci (bins) with a spatial inconsistency. |
Yoli Shavit
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).
prepareCalib
calibrate
plotInc
summaryInc
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