createDiffLogoObject {DiffLogo} | R Documentation |
Creates a DiffLogo object
createDiffLogoObject(pwm1, pwm2, stackHeight = shannonDivergence, baseDistribution = normalizedDifferenceOfProbabilities, alphabet = DNA, align_pwms = FALSE, unaligned_penalty = divergencePenaltyForUnaligned, try_reverse_complement = TRUE, base_distribution = NULL, length_normalization = FALSE, unaligned_from_left = 0, unaligned_from_right = 0)
pwm1 |
representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix |
pwm2 |
representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix |
stackHeight |
function for the height of a stack at position i |
baseDistribution |
function for the heights of the individual bases |
alphabet |
of type Alphabet |
align_pwms |
if True, will aling and extend pwms. |
unaligned_penalty |
is a function for localPwmAlignment. |
try_reverse_complement |
if True, alignment will try reverse complement pwms |
base_distribution |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |
length_normalization |
If true, will minimize the average divergence between PWMs. Otherwise will minimize the sum of divergences between positions. In both cases unalignes positions are compared to base_distribution and are counted when computing the alignment length. |
unaligned_from_left |
the number of unaligned positions on the left |
unaligned_from_right |
the number of unaligned positions on the right |
DiffLogo object
Martin Nettling
motif_folder= "extdata/pwm" motif_names = c("HepG2","MCF7","HUVEC","ProgFib") motifs = list() for (name in motif_names) { fileName = paste(motif_folder,"/",name,".pwm",sep="") file = system.file(fileName, package = "DiffLogo") motifs[[name]] = getPwmFromPwmFile(file) } pwm1 = motifs[[motif_names[[1]]]] pwm2 = motifs[[motif_names[[2]]]] diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2) diffLogo(diffLogoObj)