Import, Modify, and Export Motifs with R

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Documentation for package ‘universalmotif’ version 1.26.2

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A C 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.
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.
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.

-- E --

enrich_motifs Enrich for input motifs in a set of sequences.
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 --

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.
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.
meme_alph Sequence-related utility functions.
merge_motifs Merge motifs.
merge_similar Identify and merge similar motifs within a collection of motifs (or simply cluster motifs).
motif_peaks Look for overrepresented motif position peaks in a set of sequences.
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'.

-- N --

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

-- P --

pcm_to_ppm Motif-related utility functions.
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.
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.
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_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.

-- 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.