PWMUnscaled {PWMEnrich} | R Documentation

## Create a PWM from PFM

### Description

The PWM function from Biostrings without unit scaling

### Usage

      PWMUnscaled(x, id = "", name = "",
        type = c("log2probratio", "prob"),
        prior.params = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
        pseudo.count = prior.params, unit.scale = FALSE,
        seq.count = NULL)

### Arguments

`x` | the integer count matrix representing the motif, rows as nucleotides
`id` | a systematic ID given to this PWM, could include the source, version, etc
`name` | the name of the transcription factor (TF) to which the PWM corresponds to
`type` | the type of PWM calculation, either as log2-odds, or posterior probability (frequency matrix)
`prior.params` | the pseudocounts for each of the nucleotides
`pseudo.count` | the pseudo-count values if different from priors
`unit.scale` | if to unit.scale the pwm (default is no unit scaling)
`seq.count` | if x is a normalised PFM (i.e. with probabilities instead of sequence counts), then this sequence count will be used to convert `x` into a count matrix

### Details

By default the Biostrings package scales the log-odds score so it is within 0 and 1. In this function we take a more traditional approach with no unit scaling and offer unit scaling as an additional parameter.

See ?PWM from Biostrings for more information on input arguments.

### Value

a new PWM object representing the PWM

### Examples

    if(require("PWMEnrich.Dmelanogaster.background")){
        data(MotifDb.Dmel.PFM)

        ttk = MotifDb.Dmel.PFM[["ttk"]]

        PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk") # make a PWM with uniform background
        PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk", prior.params=c("A"=0.2, "C"=0.3, "G"=0.3, "T"=0.2)) # custom background

        prior = getBackgroundFrequencies("dm3", quick=TRUE) # get background for drosophila (quick mode on a reduced dataset)
        PWMUnscaled(ttk, id="ttk-JASPAR", name="ttk", prior.params=prior) # convert using genomic background
    }

[Package PWMEnrich version 4.16.0 Index]