Index

A

active_sites_file (built-in variable)

Alignments (class in defcom.alignment), [1]

B

bias_correction (built-in variable) bootstrap_active_set_size (built-in variable)

bootstrap_inactive_set_size (built-in variable) bootstrap_iterations (built-in variable)

C

candidate_bam_file (built-in variable) candidate_sites_file (built-in variable) combine_strands (built-in variable)

complement() (defcom.genome.Genome class method), [1] convert_to_cuts() (defcom.features.Features class method), [1]

D

defcom.alignment (module), [1] defcom.features (module), [1] defcom.genome (module), [1]

defcom.motif_sites (module), [1] defcom.performance_stats (module), [1]

F

f_offset (built-in variable) Features (class in defcom.features), [1]

flank_size (built-in variable)

G

Genome (class in defcom.genome), [1] genome_file (built-in variable) get_all_sites() (defcom.motif_sites.MotifSites method), [1] get_chr_length() (defcom.genome.Genome method), [1] get_chr_names() (defcom.genome.Genome method), [1] get_chr_sites() (defcom.motif_sites.MotifSites method), [1] get_cut_sites() (defcom.alignment.Alignments method), [1] get_genome_filename() (defcom.genome.Genome method), [1] get_mapped_read_count() (defcom.alignment.Alignments method), [1] get_pwm_scores() (defcom.features.Features class method), [1]

get_read_density() (defcom.alignment.Alignments method), [1] get_reads() (defcom.alignment.Alignments method), [1] get_sequence() (defcom.genome.Genome method), [1] get_sites() (defcom.motif_sites.MotifSites method), [1] get_slopes() (defcom.features.Features class method), [1] get_splits() (defcom.features.Features class method), [1] get_total_read_count() (defcom.alignment.Alignments method), [1] get_unmapped_read_count() (defcom.alignment.Alignments method), [1] get_weights() (defcom.alignment.Alignments method), [1]

I

inactive_sites_file (built-in variable)

M

memory_limit (built-in variable) model_data_file (built-in variable)

MotifSites (class in defcom.motif_sites), [1]

P

pAUC() (in module defcom.performance_stats), [1]

R

r_offset (built-in variable) results_file (built-in variable)

reverse_complement() (defcom.genome.Genome class method), [1]

S

slope() (defcom.features.Features class method), [1]

subsample_sites() (defcom.motif_sites.MotifSites method), [1]

T

training_active_set_size (built-in variable) training_bam_file (built-in variable)

training_inactive_set_size (built-in variable)