# RNA-binding protein motif analysis

## Documentation for package ‘transite’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.RBPMotif | An S4 class to represent a RBPMotif
.SpectrumScore | An S4 class to represent a scored spectrum
calculate_kmer_enrichment | _k_-mer Enrichment between Foreground and Background Sets
calculate_local_consistency | Local Consistency Score
calculate_motif_enrichment | Binding Site Enrichment Value Calculation
calculate_transcript_mc | Motif Enrichment calculation
check_kmers | Check Validity of Set of _k_-mers
classify_spectrum | Simple spectrum classifier based on empirical thresholds
compute_kmer_enrichment | _k_-mer Enrichment between Foreground and Background Sets
count_homopolymer_corrected_kmers | Correction for Homopolymeric Stretches
create_kmer_motif | Creates Transite motif object from character vector of _k_-mers
create_matrix_motif | Creates Transite motif object from position weight matrix
draw_volcano_plot | _k_-mer Enrichment Volcano Plot
estimate_significance | Permutation Test Based Significance of Observed Mean
estimate_significance_core | Significance of Observed Mean
ge | Toy Gene Expression Data Set
generate_iupac_by_kmers | Generates IUPAC code for a character vector of _k_-mers
generate_iupac_by_matrix | Generates IUPAC code for motif matrix
generate_kmers | _k_-mer Counts for Sequence Set
generate_kmers_from_iupac | Generates all _k_-mers for IUPAC string
generate_permuted_enrichments | Generate Random Permutations of the Enrichment Data
geometric_mean | Geometric Mean
get_adj_r_squared | An S4 class to represent a scored spectrum
get_adj_r_squared-method | An S4 class to represent a scored spectrum
get_consistency_score | An S4 class to represent a scored spectrum
get_consistency_score-method | An S4 class to represent a scored spectrum
get_consistency_score_n | An S4 class to represent a scored spectrum
get_consistency_score_n-method | An S4 class to represent a scored spectrum
get_consistency_score_p_value | An S4 class to represent a scored spectrum
get_consistency_score_p_value-method | An S4 class to represent a scored spectrum
get_heptamers | An S4 class to represent a RBPMotif
get_heptamers-method | An S4 class to represent a RBPMotif
get_hexamers | An S4 class to represent a RBPMotif
get_hexamers-method | An S4 class to represent a RBPMotif
get_id | An S4 class to represent a RBPMotif
get_id-method | An S4 class to represent a RBPMotif
get_iupac | An S4 class to represent a RBPMotif
get_iupac-method | An S4 class to represent a RBPMotif
get_model_degree | An S4 class to represent a scored spectrum
get_model_degree-method | An S4 class to represent a scored spectrum
get_model_f_statistic | An S4 class to represent a scored spectrum
get_model_f_statistic-method | An S4 class to represent a scored spectrum
get_model_f_statistic_p_value | An S4 class to represent a scored spectrum
get_model_f_statistic_p_value-method | An S4 class to represent a scored spectrum
get_model_residuals | An S4 class to represent a scored spectrum
get_model_residuals-method | An S4 class to represent a scored spectrum
get_model_slope | An S4 class to represent a scored spectrum
get_model_slope-method | An S4 class to represent a scored spectrum
get_motifs | Retrieve list of all motifs
get_motifs_meta_info | Displays motif meta information.
get_motif_by_id | Retrieve motif objects by id
get_motif_by_rbp | Retrieve motif objects by gene symbol
get_motif_matrix | An S4 class to represent a RBPMotif
get_motif_matrix-method | An S4 class to represent a RBPMotif
get_ppm | Get Position Probability Matrix (PPM) from motif object
get_rbps | An S4 class to represent a RBPMotif
get_rbps-method | An S4 class to represent a RBPMotif
get_source | An S4 class to represent a RBPMotif
get_source-method | An S4 class to represent a RBPMotif
get_species | An S4 class to represent a RBPMotif
get_species-method | An S4 class to represent a RBPMotif
get_type | An S4 class to represent a RBPMotif
get_type-method | An S4 class to represent a RBPMotif
get_width | An S4 class to represent a RBPMotif
get_width-method | An S4 class to represent a RBPMotif
init_iupac_lookup_table | Initializes the IUPAC lookup table
kmers_enrichment | Example _k_-mer Enrichment Data
motifs | Transite Motif Database
plot-method | An S4 class to represent a RBPMotif
plot-method | An S4 class to represent a scored spectrum
p_combine | P-value aggregation
RBPMotif-class | An S4 class to represent a RBPMotif
run_kmer_spma | _k_-mer-based Spectrum Motif Analysis
run_kmer_tsma | _k_-mer-based Transcript Set Motif Analysis
run_matrix_spma | Matrix-based Spectrum Motif Analysis
run_matrix_tsma | Matrix-based Transcript Set Motif Analysis
score_sequences | Score Sequences with PWM
score_spectrum | Calculates spectrum scores and creates spectrum plots
score_transcripts | Scores transcripts with position weight matrices
score_transcripts_single_motif | Scores transadsadscripts with position weight matrices
set_motifs | Set Transite motif database
show-method | An S4 class to represent a RBPMotif
show-method | An S4 class to represent a scored spectrum
SpectrumScore-class | An S4 class to represent a scored spectrum
subdivide_data | Subdivides Sequences into _n_ Bins
toy_motif_matrix | Toy Motif Matrix
transite | transite