getInfoLevelForChr: Compute the information level for a given chromosome after...
In FisHiCal: Iterative FISH-based Calibration of Hi-C Data
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Description
A function to compute the information proportions in a a given calibrated Hi-C matrix for a given chromosome. This will be the proportions of non-zero cells, representing information that was not discarded in the calibration step.
Usage
1
getInfoLevelForChr(calibHiC, hicCoord, chr)
Arguments
calibHiC
A calibrated Hi-C matrix. This matrix could be prepared with calibrate.
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.
chr
The name of the chromosome of interest (as it appears in hicCoord).
Details
The level of information can affect the accuracy of the 3D prediction, which may be lower for sparse calibration matrices (information level < 0.4).
Value
The information level for the given chromosome in the calibrated Hi-C matrix.
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
FisHiCal documentation built on May 1, 2019, 10:09 p.m.
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Description Usage Arguments Details Value Author(s) References See Also
Description
A function to compute the information proportions in a a given calibrated Hi-C matrix for a given chromosome. This will be the proportions of non-zero cells, representing information that was not discarded in the calibration step.
Usage
1 | getInfoLevelForChr(calibHiC, hicCoord, chr)
|
Arguments
calibHiC |
A calibrated Hi-C matrix. This matrix could be prepared with |
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. |
chr |
The name of the chromosome of interest (as it appears in hicCoord). |
Details
The level of information can affect the accuracy of the 3D prediction, which may be lower for sparse calibration matrices (information level < 0.4).
Value
The information level for the given chromosome in the calibrated Hi-C matrix.
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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