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Extract quantiles of pwm of intervals from a motif database

gextract_pwm.quantile.Rd

Extract for each interval its quantile in the genome for each motif given its length. Note that the quantiles are computed for each motif separately, and therefore this might be slow for intervals with un-normalized lengths.

Usage

gextract_pwm.quantile(
  intervals,
  motifs = NULL,
  dataset = MOTIF_DB,
  percision = 0.01,
  spat = NULL,
  spat_min = 1,
  spat_max = NULL,
  bidirect = TRUE,
  prior = 0.01,
  func = "logSumExp",
  n_sequences = 10000,
  dist_from_edge = 3000000,
  chromosomes = NULL,
  parallel = getOption("prego.parallel", TRUE)
)

Arguments

intervals

misha intervals set

motifs

names of specific motifs to extract from the dataset

dataset

a data frame with PSSMs ('A', 'C', 'G' and 'T' columns), with an additional column 'motif' containing the motif name, for example HOMER_motifs or JASPAR_motifs, or all_motif_datasets(), or a MotifDB object.

percision

the percision of the quantiles. Default is 0.01, which means that the quantiles will be computed for every 1% of the pwm.

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.

func

the function to use to combine the PWMs for each sequence. Either 'logSumExp' or 'max'. The default is 'logSumExp'.

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)

parallel

logical, whether to use parallel processing

Value

a data frame with the quantiles of the pwm for each interval and motif. The quantiles columns would be of the form {motif}.q

Examples

if (FALSE) { # \dontrun{
library(misha)
gdb.init_examples()
gextract_pwm.quantile("annotations", motifs = c("JASPAR.CDX1", "JASPAR.CDX2"), dist_from_edge = 100)
} # }