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

In FisHiCal: Iterative FISH-based Calibration of Hi-C Data

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.

Author(s)

Yoli Shavit

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

FisHiCal documentation built on May 1, 2019, 10:09 p.m.