prepareData: Match FISH distances and Hi-C frequencies for calibration
In FisHiCal: Iterative FISH-based Calibration of Hi-C Data

Description Usage Arguments Details Value Author(s) References See Also

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

1	prepareData(fish, fishCoord, hic, hicCoord)

`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.

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.

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.

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

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