Compute quantile of pwm for a given interval size

Computes the quantile of the pwm for a given interval size by sampling random intervals from the genome, or using given intervals. The number of sequences to sample can be specified with n_sequences.

Usage

gpwm_quantiles(
  size,
  quantiles,
  pssm,
  bg_intervals = NULL,
  spat = NULL,
  spat_min = 1,
  spat_max = NULL,
  bidirect = TRUE,
  prior = 0.01,
  n_sequences = 10000,
  dist_from_edge = 3000000,
  chromosomes = NULL,
  func = "logSumExp"
)

Arguments

size: size of the intervals to sample
quantiles: quantiles to compute. See quantile for more details.
pssm: PSSM matrix or data frame
bg_intervals: (optional) an intervals set for the background. If not provided, random intervals will be used
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.
n_sequences: number of sequences to sample in order to compute the quantiles. The default is 1e4.
dist_from_edge: The minimum distance from the edge of the chromosome for a region to start or end(default: 3e6)
chromosomes: The chromosomes to sample from (default: all chromosomes)
func: the function to use to combine the PWMs for each sequence. Either 'logSumExp' or 'max'. The default is 'logSumExp'.

Value

a named vector with the quantiles of the pwm for the given interval size.

Examples

if (FALSE) { # \dontrun{
library(misha)
library(dplyr)
gdb.init_examples()
pssm <- JASPAR_motifs %>%
    filter(motif == "JASPAR.CDX1") %>%
    select(-motif)
gpwm_quantiles(1000, seq(0, 1, 0.1), pssm, dist_from_edge = 100)
} # }