R: Compute exact position weight/count matrix score...
computeScoreDist
R Documentation
Compute exact position weight/count matrix score distribution.
Description
Computes the discretisized score distribution of a position count matrix
(PCM) or a position weight matrix (PWM), using the method described by
Rahmann et al.
Usage
computeScoreDist(motif, gc, granularity = 0.01, unit = "nat")
Arguments
motif
A matrix representing a PCM or PWM; each column a position and
each row a base corresponding to A, C, G, T. This order is assumed, unless
the rows are correspondingly named in a different order.
gc
A scalar giving the GC fraction to assume.
granularity
The granularity of the discretization, defaults to 0.01.
unit
The logarithm unit of the score computed from the PCM or PWM, can
be "nat" (default, natural logarithm), "bit" (base 2), or "dit" (base 10).
Value
a ProfileDist object
References
Rahmann, S., Mueller, T., and Vingron, M. (2003). On the power of
profiles for transcription factor binding site detection. Stat Appl Genet
Mol Biol 2, Article7.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(profileScoreDist)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/profileScoreDist/computeScoreDist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: computeScoreDist
> ### Title: Compute exact position weight/count matrix score distribution.
> ### Aliases: computeScoreDist
>
> ### ** Examples
>
> data(INR)
> thedist <- computeScoreDist(regularizeMatrix(INR), 0.5)
> plotDist(thedist)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.