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%") ## Utility functions for basic manipulation of the Position Weight Matrix maxWeights(pwm) maxScore(pwm) #reverseComplement(x, ...) # S4 method for matrix objects
pwm |
A Position Weight Matrix (integer 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 percentage (e.g. "85%" ) of the highest possible
score or as an integer.
|
An XStringViews object for matchPWM
.
A single integer for countPWM
.
An integer 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") PWMscore(pwm, subject, 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)