Generate random genome motif PSSM matrix
Usage
gen_random_genome_peak_motif_matrix(
num_peaks = 100000,
peak_width = 200,
bp_from_chrom_edge_to_avoid = 3000000,
datasets_of_interest = NULL,
motif_regex = NULL,
motif_tracks = NULL,
parallel = TRUE
)Arguments
- num_peaks
total number of intervals (will be divided proportionately between chromosomes) to use as background
- peak_width
(optional) - size of region around peak centers to extract motif energies for
- bp_from_chrom_edge_to_avoid
regions (in bp) from edges of chromosomes to avoid sampling from (e.g. avoid acrocentric centromeres)
- datasets_of_interest
(optional) - names of pssm datasets (name.key-name.data file combinations) to calculate PSSM values for
- motif_regex
(optional) - a vector of regular expressions for which to match motif track names and extract motif PSSMs
- motif_tracks
(optional) - misha track names for which to extract motif PSSMs
- parallel
(optional) - whether to use parallel computations
Examples
if (FALSE) {
random_genome_motifs <- gen_random_genome_peak_motif_matrix(num_peaks = 5e+4, datasets_of_interest = get_available_pssms(return_datasets_only = TRUE))
}