matchPWM: PWM creating, matching, and related utilities

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Position Weight Matrix (PWM) creating, matching, and related utilities for DNA data. (PWM for amino acid sequences are not supported.)

Usage

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PWM(x, type = c("log2probratio", "prob"),
    prior.params = c(A=0.25, C=0.25, G=0.25, T=0.25))

matchPWM(pwm, subject, min.score="80%", with.score=FALSE, ...)
countPWM(pwm, subject, min.score="80%", ...)
PWMscoreStartingAt(pwm, subject, starting.at=1)

## Utility functions for basic manipulation of the Position Weight Matrix
maxWeights(x)
minWeights(x)
maxScore(x)
minScore(x)
unitScale(x)
## S4 method for signature 'matrix'
reverseComplement(x, ...)

Arguments

x

For PWM: a rectangular character vector or rectangular DNAStringSet object ("rectangular" means that all elements have the same number of characters) with no IUPAC ambiguity letters, or a Position Frequency Matrix represented as an integer matrix with row names containing at least A, C, G and T (typically the result of a call to consensusMatrix).

For maxWeights, minWeights, maxScore, minScore, unitScale and reverseComplement: a Position Weight Matrix represented as a numeric matrix with row names A, C, G and T.

type

The type of Position Weight Matrix, either "log2probratio" or "prob". See Details section for more information.

prior.params

A positive numeric vector, which represents the parameters of the Dirichlet conjugate prior, with names A, C, G, and T. See Details section for more information.

pwm

A Position Weight Matrix represented as a numeric matrix with row names A, C, G and T.

subject

Typically a DNAString object. A Views object on a DNAString subject, a MaskedDNAString object, or a single character string, are also supported.

IUPAC ambiguity letters in subject are ignored (i.e. assigned weight 0) with a warning.

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.

with.score

TRUE or FALSE. If TRUE, then the score of each hit is included in the returned object in a metadata column named score. Say the returned object is hits, this metadata column can then be accessed with mcols(hits)$score.

starting.at

An integer vector specifying the starting positions of the Position Weight Matrix relatively to the subject.

...

Additional arguments for methods.

Details

The PWM function uses a multinomial model with a Dirichlet conjugate prior to calculate the estimated probability of base b at position i. As mentioned in the Arguments section, prior.params supplies the parameters for the DNA bases A, C, G, and T in the Dirichlet prior. These values result in a position independent initial estimate of the probabilities for the bases to be priorProbs = prior.params/sum(prior.params) and the posterior (data infused) estimate for the probabilities for the bases in each of the positions to be postProbs = (consensusMatrix(x) + prior.params)/(length(x) + sum(prior.params)). When type = "log2probratio", the PWM = unitScale(log2(postProbs/priorProbs)). When type = "prob", the PWM = unitScale(postProbs).

Value

A numeric matrix representing the Position Weight Matrix for PWM.

A numeric vector containing the Position Weight Matrix-based scores for PWMscoreStartingAt.

An XStringViews object for matchPWM.

A single integer for countPWM.

A vector containing the max weight for each position in pwm for maxWeights.

A vector containing the min weight for each position in pwm for minWeights.

The highest possible score for a given Position Weight Matrix for maxScore.

The lowest possible score for a given Position Weight Matrix for minScore.

The modified numeric matrix given by (x - minScore(x)/ncol(x))/(maxScore(x) - minScore(x)) for unitScale.

A PWM obtained by reverting the column order in PWM x and by reassigning each row to its complementary nucleotide for reverseComplement.

Author(s)

H. Pag<c3><a8>s and P. Aboyoun

References

Wasserman, WW, Sandelin, A., (2004) Applied bioinformatics for the identification of regulatory elements, Nat Rev Genet., 5(4):276-87.

See Also

consensusMatrix, matchPattern, reverseComplement, DNAString-class, XStringViews-class

Examples

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## Data setup:
data(HNF4alpha)
library(BSgenome.Dmelanogaster.UCSC.dm3)
chr3R <- Dmelanogaster$chr3R
chr3R

## Create a PWM from a PFM or directly from a rectangular
## DNAStringSet object:
pfm <- consensusMatrix(HNF4alpha)
pwm <- PWM(pfm)  # same as 'PWM(HNF4alpha)'

## Perform some general routines on the PWM:
round(pwm, 2)
maxWeights(pwm)
maxScore(pwm)
reverseComplement(pwm)

## Score the first 5 positions:
PWMscoreStartingAt(pwm, chr3R, starting.at=1:5)

## Match the plus strand:
hits <- matchPWM(pwm, chr3R)
nhit <- countPWM(pwm, chr3R)  # same as 'length(hits)'

## Use 'with.score=TRUE' to get the scores of the hits:
hits <- matchPWM(pwm, chr3R, with.score=TRUE)
head(mcols(hits)$score)
min(mcols(hits)$score / maxScore(pwm))  # should be >= 0.8

## The scores can also easily be post-calculated:
scores <- PWMscoreStartingAt(pwm, subject(hits), start(hits))

## Match the minus strand:
matchPWM(reverseComplement(pwm), chr3R)

Biostrings documentation built on June 2, 2017, 2:01 a.m.

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