ggnomics
ggnomics copied to clipboard
Stat functions for Hi-C
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.
The eigen, cor and cov stats might just work for any matrix