paffinity: compute p-values for affinity values

In matthuska/tRap: A biophysical model for transcription factor binding affinities

Description

Use generalized extreme value distributions fitted for each matrix to compute p-values of trap affinities.

Usage

paffinity(affinity, matrix.name, len, params = NULL, no.exact = FALSE)

Arguments

affinity	trap affinity value
matrix.name	name of the transfac matrix (ignored if params not NULL)
len	length of the region used to compute the affinity
params	if params is NULL (default), precomputed parameters will be loaded otherwise params are c(shape, scale, loc) given to the generalized extreme value distribution
no.exact	do not use the parameters that were learned for sequences of the exact same length as len

Details

given the affinity compute the p value for the matrix and the length len if params is NULL, precomputed parameters will be loaded other wise params are c(shape, scale, loc) given to the generalized extreme value distribution

Value

p-value of the affinity score(s)

References

Thomas Manke et.al.

Examples

## Not run: 
matrices = read.transfac.dir(dir)
seq = read some fasta or get from BSgenome package
matrix.name = "AP1.."
af = affinity(matrices[[matrix.name]], seq)
paffinity(af, matrix.name, 200)
## End(Not run)

matthuska/tRap documentation built on May 21, 2019, 1:23 p.m.