# Import, Modify, and Export Motifs with R

## Documentation for package ‘universalmotif’ version 1.31.42

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

## Help Pages

A C D E F G I J L M N P R S T U V W misc

universalmotif-package | universalmotif: Import, Modify and Export Motifs with R

## -- A --

add_gap | Motif-related utility functions.
add_multifreq | Add multi-letter information to a motif.
annotate_logo | Embed motif logos in ggplot2 constructions.
annotate_motif | Embed motif logos in ggplot2 constructions.
ArabidopsisMotif | Arabidopsis motif in 'universalmotif' format.
ArabidopsisPromoters | Arabidopsis promoters as a 'DNAStringSet'.
as.data.frame-method | universalmotif: Motif class.
average_ic | Motif-related utility functions.

## -- C --

calc_complexity | Sequence-related utility functions.
calc_windows | Sequence-related utility functions.
cbind-method | universalmotif: Motif class.
colMeans-method | universalmotif: Motif class.
colnames-method | universalmotif: Motif class.
colSums-method | universalmotif: Motif class.
compare_columns | Motif-related utility functions.
compare_motifs | Compare motifs.
compare_motifs_lite | Faster minimalist motif comparison.
consensus_to_ppm | Motif-related utility functions.
consensus_to_ppmAA | Motif-related utility functions.
convert_motifs | Convert motif class.
convert_motifs-method | Convert motif class.
convert_type | Convert universalmotif type.
count_klets | Sequence-related utility functions.
create_motif | Create a motif.
create_motif-method | Create a motif.
create_sequences | Create random sequences.

## -- D --

dedup_hits | Deduplicate overlapping motif hits.

## -- E --

enrich_motifs | Enrich for input motifs in a set of sequences.
enrich_motifs_lite | Fast minimalist motif enrichment.
examplemotif | Example motif in 'universalmotif' format.
examplemotif2 | Another example motif in 'universalmotif' format.

## -- F --

filter_motifs | Filter a list of motifs.
fontDFroboto | Polygon coordinates for plotting letters.

## -- G --

GeomMotif | Embed motif logos in ggplot2 constructions.
geom_logo | Embed motif logos in ggplot2 constructions.
geom_motif | Embed motif logos in ggplot2 constructions.
get_bkg | Calculate sequence background.
get_consensus | Motif-related utility functions.
get_consensusAA | Motif-related utility functions.
get_klets | Sequence-related utility functions.
get_matches | Motif-related utility functions.
get_scores | Motif-related utility functions.

## -- I --

icm_to_ppm | Motif-related utility functions.
implant_motifs | Implant sampled motif instances into sequences at known positions.
initialize-method | universalmotif: Motif class.

## -- J --

JASPAR2018_CORE_DBSCORES | JASPAR2018 CORE database scores

## -- L --

log_string_pval | Motif-related utility functions.

## -- M --

make_DBscores | Create P-value databases.
mask_ranges | Sequence-related utility functions.
mask_seqs | Sequence-related utility functions.
match_bkg | Sample composition-matched background sequences from a universe.
meme_alph | Sequence-related utility functions.
merge_motifs | Merge motifs.
merge_motifs_lite | Merge a list of motifs into a single consensus motif.
merge_similar | Identify and merge similar motifs within a collection of motifs (or simply cluster motifs).
merge_similar_lite | Cluster similar motifs by significance and merge each cluster.
motif_coocc | Find significantly co-occurring motif pairs in a set of sequences.
motif_finder | Discover _de novo_ motifs in a set of sequences.
motif_peaks | CentriMo-style positional enrichment of motif hits.
motif_proximity | Test for motif enrichment near a set of genomic anchors.
motif_pvalue | Motif P-value and scoring utility
motif_range | Motif-related utility functions.
motif_rc | Get the reverse complement of a DNA or RNA motif.
motif_score | Motif-related utility functions.
motif_tree | Generate 'ggplot2' motif trees with 'ggtree'.
motif_tree_lite | Generate ggtree-based motif trees using 'compare_motifs_lite()'.

## -- N --

ncol-method | universalmotif: Motif class.
normalize-method | universalmotif: Motif class.
nrow-method | universalmotif: Motif class.

## -- P --

pcm_to_ppm | Motif-related utility functions.
plot_match_bkg | Visualise composition match between target and background sequences.
plot_motif_peaks | Plot the position distribution of motif hits.
plot_motif_proximity | Plot the distance-to-anchor distribution of motif hits.
position_icscore | Motif-related utility functions.
ppm_to_icm | Motif-related utility functions.
ppm_to_pcm | Motif-related utility functions.
ppm_to_pwm | Motif-related utility functions.
prob_match | Motif-related utility functions.
prob_match_bkg | Motif-related utility functions.
pwm_to_ppm | Motif-related utility functions.

## -- R --

read_cisbp | Import CIS-BP motifs.
read_homer | Import HOMER motifs.
read_jaspar | Import JASPAR motifs.
read_matrix | Import motifs from raw matrices.
read_meme | Import MEME motifs.
read_motifs | Import universalmotif formatted motifs.
read_transfac | Import TRANSFAC motifs.
read_uniprobe | Import UNIPROBE motifs.
requires_update | Tidy manipulation of motifs.
round_motif | Motif-related utility functions.
rowMeans-method | universalmotif: Motif class.
rownames-method | universalmotif: Motif class.
rowSums-method | universalmotif: Motif class.
run_meme | Run MEME from within R.

## -- S --

sample_sites | Generate binding sites from a motif.
scan_sequences | Scan sequences for matches to input motifs.
scan_sequences_lite | Faster minimalist motif scanner.
score_match | Motif-related utility functions.
sequence_complexity | Calculate sequence complexity.
show-method | universalmotif: Motif class.
shuffle_motifs | Shuffle motifs by column.
shuffle_sequences | Shuffle input sequences.
shuffle_string | Sequence-related utility functions.
slide_fun | Sequence-related utility functions.
StatLogo | Embed motif logos in ggplot2 constructions.
StatMotif | Embed motif logos in ggplot2 constructions.
subset-method | universalmotif: Motif class.
summarise_motifs | Motif-related utility functions.
switch_alph | Switch between DNA and RNA alphabets.

## -- T --

tidy-motifs | Tidy manipulation of motifs.
to_df | Tidy manipulation of motifs.
to_list | Tidy manipulation of motifs.
trim_cwm | Trim CWM motifs by absolute column sum.
trim_motifs | Trim motifs.

## -- U --

ungap | Motif-related utility functions.
universalmotif | universalmotif: Motif class.
universalmotif-class | universalmotif: Motif class.
universalmotif-pkg | universalmotif: Import, Modify and Export Motifs with R
update_motifs | Tidy manipulation of motifs.
utilities | Utility functions.
utils-motif | Motif-related utility functions.
utils-sequence | Sequence-related utility functions.

## -- V --

view_logo | Plot logos from numeric matrices.
view_motifs | Plot motif logos.
view_motifs_lite | Plot motif logos using 'compare_motifs_lite()' alignment (v2).

## -- W --

window_string | Sequence-related utility functions.
write_homer | Export motifs in HOMER format.
write_jaspar | Export motifs in JASPAR format.
write_matrix | Export motifs as raw matrices.
write_meme | Export motifs in MEME format.
write_motifs | Export motifs in universalmotif format.
write_transfac | Export motifs in TRANSFAC format.

## -- misc --

[-method | universalmotif: Motif class.
[<--method | universalmotif: Motif class.