empiricalPvalueSequenceSet {PWMEnrich} | R Documentation |
Calculate empirical P-value for a set of sequences, using either affinity or cutoff. When cutoff is used, the score is a number of motif hits above a certain log-odds cutoff.
empiricalPvalueSequenceSet( scores, seq.len, pwm.len, bg.fwd, bg.rev, cutoff = NULL, B = 10000, verbose = FALSE )
scores |
a matrix of scores, rows for sequences, columns for PWMs |
seq.len |
the lengths of sequences |
pwm.len |
the lengths of PWMs |
bg.fwd |
raw odds scores for the forward strand of background |
bg.rev |
raw odds scores for the reverse strand of background |
cutoff |
if not NULL, will use hit count above this cutoff. The cutoff should be specified in log2. |
B |
the number of random replicates |
verbose |
if to give verbose progress reports |