multipleLocalPwmsAlignment {DiffLogo} | R Documentation |
Creates a multiple alignment of pwms
multipleLocalPwmsAlignment(pwms, divergence = shannonDivergence, unaligned_penalty = divergencePenaltyForUnaligned, try_reverse_complement = TRUE, base_distribution = NULL, length_normalization = FALSE)
pwms |
list of pwms |
divergence |
Divergence measure. |
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. |
list
Lando Andrey
file1 = system.file("extdata/homer/Max.motif", package = "DiffLogo") file2 = system.file("extdata/homer/c-Myc.motif", package = "DiffLogo") pwm1 = getPwmFromFile(file1) pwm2 = getPwmFromFile(file2) multiple_pwms_alignment = multipleLocalPwmsAlignment(list(pwm1, pwm2))