pwm: Generate a PWM for a set of sequences

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Generate a PWM for a set of sequences

Description

Generate a PWM for a set of sequences

Usage

pwm(seqs, chars = c("C", "G", "T", "A"), priors = table(chars) - 1)

Arguments

seqs	vector of strings, sequences to form a position weight matrix from (all same length)
chars	allowed characters
priors	additional counts to add to each column with (default is a lazy way to get a named 0 vector)

Value

position weight matrix with length(chars) rows and nchar(seqs) columns

Examples

pwm(c('ACTG','ACTT','ACTT','ACGT'))
pwm(c('ACTG','ACTT','ACTT','ACGT'),priors=c('C'=1,'G'=1,'T'=1,'A'=1))

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.