Compute Motif Energies

This function computes motif energies for given peak intervals using a specified motif database. Optionally, it can normalize the computed motif energies using additional normalization intervals.

Usage

compute_motif_energies(
  peak_intervals,
  db = iceqream::motif_db,
  normalization_intervals = peak_intervals,
  prior = 0.01,
  normalize = TRUE,
  energy_norm_quantile = 1,
  norm_energy_max = 10,
  min_energy = -7,
  db_quantiles = NULL
)

Arguments

peak_intervals

A data frame containing the peak intervals with columns: chrom, start, and end. If an additional column 'peak_name' is present, it will be used as row names in the output matrix.

db

A motif database to use for extracting motif energies. Default is iceqream::motif_db.

normalization_intervals

A data frame containing intervals for normalization. Default is peak_intervals.

prior

a prior probability for each nucleotide.

normalize

A logical value indicating whether to normalize the motif energies. Default is TRUE.

energy_norm_quantile

A numeric value for the quantile used in normalization. Default is 1.

norm_energy_max

The maximum value to which the normalized energy values are scaled. Default is 10.

min_energy

The minimum energy value to be assigned after normalization. Default is -7.

db_quantiles

A matrix of motif energies quantiles to use for normalization. Rows are motifs and columns are quantiles. If not NULL, this would be used instead of computing the quantiles from the normalization intervals. A precomputed matrix for mouse gastrulation can be found in iceqream::mouse_db_quantiles.

Value

A matrix of motif energies.