Chromatin normalization

VCnorm(M, **kwargs)[source]

Performs vanilla coverage normalization on matrix M.

SQRTVCnorm(M, **kwargs)[source]

Performs square-root vanilla coverage normalization on matrix M.

Filenorm(M, **kwargs)[source]

Performs normalization on matrix M given a file. filename specifies the path to the file. The file should be one-column, and ideally has the same number of entries with the size of M (extra entries will be ignored). Say F is vector of the normalization factors, N is the normalized matrix, if expected is True, N[i,j] = M[i,j]/F[i]/F[j]. If expected is True, N[i,j] = M[i,j]/F[|i-j|].

SCN(M, **kwargs)[source]

Performs Sequential Component Normalization on matrix M.

[AC12]Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J. Normalization of a chromosomal contact map. BMC Genomics 2012.