PWM: Construct position weight matrix

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

Description

Makes a position weight matrix given aligned sequences.

Usage

PWM(seqs, pseudocount = 0.01, relative.freq = T, is.kinase.pwm = T,
  priors = AA_PRIORS_HUMAN, do.pseudocounts = F)

Arguments

seqs	Aligned sequences all of the same length
pseudocount	Pseudocount factor. Final pseudocount is background probability * this factor
relative.freq	Set to TRUE if each column should be divided by the sum
is.kinase.pwm	Set to TRUE if matrix is being built for a kinase
priors	Named character vector containing priors of amino acids.
do.pseudocounts	TRUE if we are to add pseudocounts

Examples

# No examples

omarwagih/rmimp documentation built on May 18, 2020, 3:11 p.m.