Package index • prego

Motif Regression

regress_multiple_motifs() regress_pwm(): Perform a PWM regression

regress_pwm.clusters(): Run PWM regression on clusters

regress_pwm.cv(): Cross-validate a PWM regression model

regress_pwm.sample(): Run PWM regression on a sample of the data

plot_regression_prediction(): Plot response variable averages vs the regression model's prediction

plot_regression_prediction_binary(): Plot the cumulative of the regression model's prediction stratified by the response variable

plot_regression_qc(): Plot the regression results

plot_regression_qc_multi(): Plot the regression results for multiple motifs

plot_spat_model(): Plot spatial model of the regression result

export_multi_regression(): Export a multiple motif regression model

export_regression_model(): Export a motif regression model

load_multi_regression(): Load a multiple motif regression model from a file

load_regression_model(): Load a motif regression model from a file

kmers

screen_kmers(): Screen for kmers

generate_kmers(): Generate kmers

kmer_matrix(): Generate a kmer Matrix

kmers_to_pssm(): Transform k-mers to PSSM (Position-Specific Scoring Matrix)

MotifDB

MotifDB-class: MotifDB Class

as.data.frame(<MotifDB>): Convert a MotifDB object to a data frame

as.matrix(<MotifDB>): Convert a MotifDB object to a matrix

initialize(<MotifDB>): Initialize method for MotifDB objects

length(<MotifDB>): Get the length of a MotifDB object

names(<MotifDB>): Get the names of motifs in a MotifDB object

plot(<MotifDB>): Plot a motif from a MotifDB object

prior(<MotifDB>): Get the prior value from a MotifDB object

`prior<-`(<MotifDB>): Set a new prior for a MotifDB object

show(<MotifDB>): Show method for MotifDB objects

`[`(<MotifDB>): Get specific motifs from the MotifDB

MOTIF_DB: A MotifDB object with motifs from all bundled databases

motif_db_to_dataframe(): Convert a MotifDB object back to a tidy data frame

`prior<-`(): Set the prior for a MotifDB object

prior(): Get or set the prior for a MotifDB object

create_motif_db(): Create a MotifDB object from a tidy data frame

PSSM/PWM utils

compute_pwm(): Compute PWMs for a set of sequences given a PSSM matrix

extract_pwm_old() extract_pwm(): Extract pwm of sequences from a motif database

gextract_pwm_old() gextract_pwm(): Extract pwm of intervals from a motif database

consensus_from_pssm(): Convert PSSM to consensus sequence

pssm_diff(): Compute KL divergence between two PSSMs

pssm_match(): Match PSSM to a directory of motifs

pssm_cor(): Compute the correlation between two given PSSMs

plot_pssm_logo(): Plot LOGO of the pssm result from the regression

plot_pssm_logo_dataset(): Plot LOGO of pssm from dataset (e.g. "HOMER" or "JASPAR")

all_motif_datasets(): Get a data frame of all the motif datasets bundled with prego

screen_pwm(): Screen for motifs in a database given a response variable

screen_pwm.clusters(): Screen for motifs in a database for every cluster

get_motif_pssm(): Extract pssm of sequences from a motif database

HOCOMOCO_motifs: PSSMs from the HOCOMOCO motif database

HOMER_motifs: PSSMs from the HOMER motif database

JASPAR_motifs: PSSMs from the JASPAR motif database

JOLMA_motifs: PSSMs from the Jolma et al. motif database

regress_multiple_motifs() regress_pwm(): Perform a PWM regression

compute_local_pwm(): Compute local PWMs for a set of sequences given a PSSM matrix

gextract_pwm.quantile(): Extract quantiles of pwm of intervals from a motif database

gpwm_quantiles(): Compute quantile of pwm for a given interval size

mask_sequences_by_pwm(): Mask sequences by thresholding the PWM

trim_pssm(): Trim PSSM

bits_per_pos(): Calculate the number of bits per position in a Position-Specific Scoring Matrix (PSSM).

calc_seq_pwm(): Calculate Position Weight Matrix (PWM) Scores for DNA Sequences

pssm_dataset_cor(): Compute a correlation matrix for a pssm dataset

pssm_rc(): Reverse complement a PSSM

pssm_to_kmer(): Transform PSSM (Position-Specific Scoring Matrix) to a KMER

rc(): Reverse Complement DNA Sequences

Sequence utils

intervals_to_seq(): Convert intervals to sequences

calc_sequences_dinuc_dist(): Calculate Dinucleotide Distribution in Sequences

calc_sequences_dinucs(): Calculate Dinucleotide Counts for Sequences

calc_sequences_trinuc_dist(): Calculate Trinucleotide Distribution in Sequences

Local PWM

gintervals.center_by_pssm(): Center intervals by PSSM

gextract.local_pwm(): Extracts local position weight matrix (PWM) scores for given intervals and a PWM.

gextract.local_pwm_freq(): Calculate the frequency of a position weight matrix (PWM) in a given set of intervals

other

motif_enrichment(): Calculate motif enrichment

sample_quantile_matched_rows(): Sample rows respecting quantiles of a reference distribution

set_parallel(): Set parallel threads

cluster_mat_example cluster_sequences_example clusters_example response_mat_example sequences_example: Dataset examples