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teunbrand / ggnomics

A small project to add ggplot2 extensions
https://teunbrand.github.io/ggnomics/
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Stat functions for Hi-C #25

Open teunbrand opened 5 years ago

teunbrand commented 5 years ago

Mainly for the fill values of the matrix.

hic_obsexp: A kind of observed over expected transformation for fill values. Would be possible to add a kind of decay parameter that takes a vector of pre-computed normalisation values. For example those derived from all chromosomes or that particular chromosome arm.

hic_diff: only in case a second experiment has been defined, could take the difference between exp1 and exp2 and output that as a computed variable.

hic_eigen: performs eigenvalue decomposition on the matrix. Can have as argument which eigenvalues to retain.

hic_cor calculates the correlation matrix of the Hi-C map

hic_cov calculates the covariance matrix of the Hi-C map

Ideally there would be some elegant way to perform subsequent stat transformations such that e.g. the eigenvalue decomposition can be performed on the hic_obsexp values or hic_cov values.

teunbrand commented 5 years ago

The eigen, cor and cov stats might just work for any matrix