motifIC {PWMEnrich} | R Documentation |
Information content for a PWM or PFM
motifIC(motif, prior.params = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25), bycol = FALSE)
motif |
a matrix of frequencies, or a PWM object |
prior.params |
the prior parameters to use when a matrix is given (ignored if motif is already a PWM) |
bycol |
if to return values separately for each column |
information content in bits (i.e. log2)
if(require("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel) data(MotifDb.Dmel.PFM) # the nucleotide distribution is taken from the PWM (in this case genomic background) motifIC(MotifDb.Dmel[["ttk"]]) # information content with default uniform background because the input is a matrix, not PWM object motifIC(MotifDb.Dmel.PFM[["ttk"]]) }