scanWithPWM {PWMEnrich} | R Documentation |
The whole sequence is scanned with a PWM and scores returned beginning at each position. Partial motif matches are not done, thus the last #[length of motif]-1 scores are NA.
scanWithPWM(pwm, dna, pwm.rev = NULL, odds.score = FALSE, both.strands = FALSE, strand.fun = "mean")
pwm |
PWM object |
dna |
a DNAString or other sequence from Biostrings |
pwm.rev |
the reverse complement for a pwm (if it is already pre-computed) |
odds.score |
if to return raw scores in odds (not logodds) space |
both.strands |
if to return results on both strands |
strand.fun |
which function to use to summarise values over two strands (default is "mean") |
The function returns either an odds average (*not* log-odds average), maximal score on each strand, or scores on both strands.
The function by default returns the score in log2
following the package Biostrings
.
a vector representing scores starting at each position, or a matrix with score in the two strands
if(require("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel) ttk = MotifDb.Dmel[["ttk"]] scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT")) # odds average over the two strands expressed as log2-odds scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT"), both.strands=TRUE) # log2-odds scores on both strands }