FisHiCal (version 1.1)

findMatchingIndices: Find matching Hi-C bins for FISH probes, using mid-points

Description

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.

Usage

findMatchingIndices(fishCoord, hicCoord)

Arguments

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.

Value

The indices of matching Hi-C bins in the given hicCoord data frame.

References

Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).

See Also

prepareData