findMatchingIndices {FisHiCal} | R Documentation |
A function for finding matching indices of Hi-C bins for FISH probes, based on the mid-points of their coordinates. Given the start and end coordinates of a set of FISH probes, the function finds the matching Hi-C bins and returns their indices in the given hicCoord data frame.
findMatchingIndices(fishCoord, hicCoord)
fishCoord |
The genomic coordinates of the FISH probes. A data frame with the following columns: chr (chromosome name), start (start position), end (end position). Additional columns are permitted but will not be used. Note that chromosome names should match between hicCoord and fishCoord. |
hicCoord |
The genomic coordinates of the 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. Note that chromosome names should match between hicCoord and fishCoord. |
The indices of matching Hi-C bins in the given hicCoord data frame.
Yoli Shavit
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).