matchPWM {Biostrings} | R Documentation |
A function implementing a simple algorithm for matching a set of patterns represented by a Position Weight Matrix (PWM) to a DNA sequence. PWM for amino acid sequences are not supported.
matchPWM(pwm, subject, min.score="80%") countPWM(pwm, subject, min.score="80%") PWMscoreStartingAt(pwm, subject, starting.at=1) ## Utility functions for basic manipulation of the Position Weight Matrix maxWeights(pwm) maxScore(pwm) ## S4 method for signature 'matrix': reverseComplement(x, ...)
pwm, x |
A Position Weight Matrix (numeric matrix with row names A, C, G and T). |
subject |
A DNAString object containing the subject sequence. |
min.score |
The minimum score for counting a match.
Can be given as a character string containing a percentage (e.g.
"85%" ) of the highest possible score or as a single number.
|
starting.at |
An integer vector specifying the starting positions of the Position Weight Matrix relatively to the subject. |
... |
Additional arguments are currently ignored by the reverseComplement
method for matrix objects.
|
An XStringViews object for matchPWM
.
A single integer for countPWM
.
A numeric vector containing the Position Weight Matrix-based scores
for PWMscoreStartingAt
.
A vector containing the max weight for each position in pwm
for maxWeights
.
The highest possible score for a given Position Weight Matrix for
maxScore
.
A PWM obtained by reverting the column order in PWM x
and by
reassigning each row to its complementary nucleotide
for reverseComplement
.
matchPattern
,
reverseComplement
,
DNAString-class,
XStringViews-class
pwm <- rbind(A=c( 1, 0, 19, 20, 18, 1, 20, 7), C=c( 1, 0, 1, 0, 1, 18, 0, 2), G=c(17, 0, 0, 0, 1, 0, 0, 3), T=c( 1, 20, 0, 0, 0, 1, 0, 8)) maxWeights(pwm) maxScore(pwm) reverseComplement(pwm) subject <- DNAString("AGTAAACAA") PWMscoreStartingAt(pwm, subject, starting.at=c(2:1, NA)) library(BSgenome.Dmelanogaster.UCSC.dm3) chr3R <- unmasked(Dmelanogaster$chr3R) chr3R ## Match the plus strand matchPWM(pwm, chr3R) countPWM(pwm, chr3R) ## Match the minus strand matchPWM(reverseComplement(pwm), chr3R)