Compute spatial frequency of motifs in trajectory model
compute_traj_model_spatial_freq.RdThis function computes the spatial frequency of motifs in a trajectory model, using the top and bottom 10% of peaks based on diff_score.
Usage
compute_traj_model_spatial_freq(
traj_model,
size,
pwm_threshold = 7,
pwm_q_threshold = 0.99,
top_q = 0.1,
bottom_q = 0.1,
atac_track = NULL,
parallel = TRUE,
bidirect_size = NULL,
k4me3_track = NULL,
k27me3_track = NULL,
k27ac_track = NULL,
orient_to_intervals = NULL,
align_to_max = TRUE,
motifs = names(traj_model@motif_models)
)Arguments
- traj_model
A trajectory model object
- size
The size of the region to compute spatial frequency for
- pwm_threshold
The threshold for the PWM score
- pwm_q_threshold
The genomic quantile to use for the PWM threshold. Would be used if
pwm_thresholdis NULL.- top_q
The proportion of top peaks to select
- bottom_q
The proportion of bottom peaks to select
- atac_track
name of ATAC-seq marginal track
- parallel
Whether to use parallel processing
- bidirect_size
Size of the intervals to use for deciding the directionality of the sequence
- k4me3_track
name of k4me3 track
- k27me3_track
name of k27me3 track
- k27ac_track
name of k27ac track
- orient_to_intervals
A data frame containing the intervals to orient the sequences to
- align_to_max
A logical indicating whether to align the sequences to the maximum in each sequence at the epigenetic tracks and atac signal
- motifs
A vector of motif names to compute spatial frequency for. Default is all motifs in the trajectory model.