| 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"]])
}