prepareData: Match FISH distances and Hi-C frequencies for calibration

Description

A function to match FISH distances and Hi-C frequencies based on matching probe/bin coordinates.

Usage

prepareData(fish, fishCoord, hic, hicCoord)

Arguments

fish

A N*N matrix giving the pairwise FISH distances between the probes defined by fishCoord. Off-diagonal zero values stand for missing distances.

fishCoord

The genomic coordinates of the N 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.

hic

A M*M matrix giving the pairwise Hi-C contact frequencies between the genomic bins defined by hicCoord. Off-diagonal zero values stand for missing frequencies.

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. Note that chromosome names should match between hicCoord and fishCoord.

Value

A data frame of matching FISH distances and Hi-C frequencies, sorted in increasing order by distance value. First column is named distances, giving the FISH distances values. Second column is named frequencies, giving the matching Hi-C frequencies values.

Details

This function calls findMatchingIndices in order to find matching Hi-C bins for FISH probes. When several FISH probes are mapped to the same bin i, the FISH distances for this bin with another bin j are not unique. In these cases the minimal non-zero FISH distance between i and j is taken as representative, in order to generate a unique match and since Hi-C is likely to be biased towards shorter distances.

References