Index

Symbols

--bam_offset detect command line option learn_dm command line option --batch_size detect command line option learn_dm command line option posterior command line option --bias_model_file detect command line option learn_dm command line option --dispersion_model_file detect command line option --exp_cutoff learn_beta command line option --fdr_cutoff learn_beta command line option posterior command line option --fdr_shuffle_n detect command line option --half_win_width detect command line option learn_dm command line option --histograms plot_dm command line option --keep_dups detect command line option learn_dm command line option

--keep_qcfail detect command line option learn_dm command line option --min_qual detect command line option learn_dm command line option --n_threads detect command line option learn_dm command line option posterior command line option --outfile learn_beta command line option learn_dm command line option plot_dm command line option --outprefix detect command line option posterior command line option --post_cutoff posterior command line option --seed detect command line option --smooth_clip detect command line option --smooth_half_win_width detect command line option --write_footprints detect command line option

B

BAM_FILE detect command line option learn_dm command line option bamfile (class in footprint_tools.cutcounts) base64decode() (in module footprint_tools.modeling.dispersion)

base64encode() (in module footprint_tools.modeling.dispersion) BEDGRAPH_FILE learn_beta command line option bias_model (class in footprint_tools.modeling.bias) bisect() (in module footprint_tools.stats.utils)

C

close() (footprint_tools.cutcounts.bamfile method) compute() (footprint_tools.modeling.predict.prediction method) compute_delta_prior() (in module footprint_tools.stats.posterior)

compute_log_prior_t() (in module footprint_tools.stats.differential) compute_logpmf_values() (in module footprint_tools.stats.differential) compute_prior_weighted() (in module footprint_tools.stats.posterior)

D

detect command line option --bam_offset --batch_size --bias_model_file --dispersion_model_file --fdr_shuffle_n --half_win_width --keep_dups --keep_qcfail --min_qual --n_threads --outprefix --seed --smooth_clip --smooth_half_win_width --write_footprints BAM_FILE FASTA_FILE INTERVAL_FILE

dispersion_model (class in footprint_tools.modeling.dispersion) DISPERSION_MODEL_FILE plot_dm command line option

E

ERROR_5PROXIMITY (footprint_tools.cutcounts.ReadError attribute) ERROR_ALIGNMENT (footprint_tools.cutcounts.ReadError attribute)

ERROR_BASEQ (footprint_tools.cutcounts.ReadError attribute) ERROR_GENOTYPE (footprint_tools.cutcounts.ReadError attribute) ERROR_MISMATCH (footprint_tools.cutcounts.ReadError attribute)

F

FASTA_FILE detect command line option learn_dm command line option fishers_combined() (in module footprint_tools.stats.windowing) fit_mu() (footprint_tools.modeling.dispersion.dispersion_model method) fit_r() (footprint_tools.modeling.dispersion.dispersion_model method) footprint_tools.cutcounts module footprint_tools.modeling.bias module footprint_tools.modeling.dispersion module

footprint_tools.modeling.predict module footprint_tools.stats.differential module footprint_tools.stats.posterior module footprint_tools.stats.utils module footprint_tools.stats.windowing module

G

GenotypeError

H

h (footprint_tools.modeling.dispersion.dispersion_model attribute)

I

INTERVAL_FILE detect command line option learn_dm command line option posterior command line option

K

kmer_model (class in footprint_tools.modeling.bias)

L

learn_beta command line option --exp_cutoff --fdr_cutoff --outfile BEDGRAPH_FILE learn_dispersion_model() (in module footprint_tools.modeling.dispersion) learn_dm command line option --bam_offset --batch_size --bias_model_file --half_win_width --keep_dups --keep_qcfail --min_qual --n_threads --outfile BAM_FILE FASTA_FILE INTERVAL_FILE

load_dispersion_model() (in module footprint_tools.modeling.dispersion) log_likelihood() (in module footprint_tools.stats.posterior) log_pmf_values() (footprint_tools.modeling.dispersion.dispersion_model method) log_pmf_values_0() (footprint_tools.modeling.dispersion.dispersion_model method) lookup() (footprint_tools.cutcounts.bamfile method) lookup_allelic() (footprint_tools.cutcounts.bamfile method)

M

metadata (footprint_tools.modeling.dispersion.dispersion_model attribute) module footprint_tools.cutcounts footprint_tools.modeling.bias footprint_tools.modeling.dispersion footprint_tools.modeling.predict footprint_tools.stats.differential footprint_tools.stats.posterior footprint_tools.stats.utils footprint_tools.stats.windowing

mu_params (footprint_tools.modeling.dispersion.dispersion_model attribute)

O

offset() (footprint_tools.modeling.bias.bias_model method)

P

p (footprint_tools.modeling.dispersion.dispersion_model attribute) p_values() (footprint_tools.modeling.dispersion.dispersion_model method) piecewise_five() (in module footprint_tools.modeling.dispersion) piecewise_four() (in module footprint_tools.modeling.dispersion) piecewise_three() (in module footprint_tools.modeling.dispersion) plot_dm command line option --histograms --outfile DISPERSION_MODEL_FILE pmf_values() (footprint_tools.modeling.dispersion.dispersion_model method) pmf_values_0() (footprint_tools.modeling.dispersion.dispersion_model method) posterior command line option --batch_size --fdr_cutoff --n_threads --outprefix --post_cutoff INTERVAL_FILE SAMPLE_DATA_FILE

posterior() (in module footprint_tools.stats.posterior) predict() (footprint_tools.modeling.bias.bias_model method) prediction (class in footprint_tools.modeling.predict) probs() (footprint_tools.modeling.bias.kmer_model method) (footprint_tools.modeling.bias.uniform_model method) product() (in module footprint_tools.stats.windowing)

R

r (footprint_tools.modeling.dispersion.dispersion_model attribute) r_params (footprint_tools.modeling.dispersion.dispersion_model attribute) read_model() (footprint_tools.modeling.bias.kmer_model method)

read_pair_generator() (footprint_tools.cutcounts.bamfile method) ReadError reverse_complement() (in module footprint_tools.modeling.predict)

S

sample() (footprint_tools.modeling.dispersion.dispersion_model method) SAMPLE_DATA_FILE posterior command line option

segment() (in module footprint_tools.stats.utils) shuffle() (footprint_tools.modeling.bias.bias_model method) stouffers_z() (in module footprint_tools.stats.windowing) sum() (in module footprint_tools.stats.windowing)

U

uniform_model (class in footprint_tools.modeling.bias)

V

validate_read() (footprint_tools.cutcounts.bamfile method)

W

weighted_stouffers_z() (in module footprint_tools.stats.windowing)

write_dispersion_model() (in module footprint_tools.modeling.dispersion)