Extracts local position weight matrix (PWM) scores for given intervals and a PWM.

Extracts local position weight matrix (PWM) scores for given intervals and a PWM.

Usage

gextract.local_pwm(
  intervals,
  pssm,
  spat = NULL,
  spat_min = 0,
  spat_max = NULL,
  bidirect = TRUE,
  prior = 0.01
)

Arguments

intervals

The intervals to extract

pssm

a PSSM matrix or data frame. The columns of the matrix or data frame should be named with the nucleotides ('A', 'C', 'G' and 'T').

spat

a data frame with the spatial model (as returned from the $spat slot from the regression). Should contain a column called 'bin' and a column called 'spat_factor'.

spat_min

the minimum position to use from the sequences. The default is 1.

spat_max

the maximum position to use from the sequences. The default is the length of the sequences.

bidirect

is the motif bi-directional. If TRUE, the reverse-complement of the motif will be used as well.

prior

a prior probability for each nucleotide.

Value

A matrix with nrow(intervals) rows and ncol(pssm) columns with the local PWM for each sequence in each position.