enrich_motifs {universalmotif} | R Documentation |
Given a set of target and background sequences, test if the input motifs are significantly enriched in the targets sequences relative to the background sequences.
enrich_motifs(motifs, sequences, bkg.sequences, search.mode = "hits", max.p = 1e-05, max.q = 1e-05, max.e = 0.001, qval.method = "fdr", positional.test = "t.test", threshold = 0.001, threshold.type = "pvalue", verbose = 1, RC = FALSE, use.freq = 1, shuffle.k = 2, shuffle.method = "linear", shuffle.leftovers = "asis", return.scan.results = FALSE, progress = TRUE, BP = FALSE)
motifs |
See |
sequences |
|
bkg.sequences |
|
search.mode |
|
max.p |
|
max.q |
|
max.e |
|
qval.method |
|
positional.test |
|
threshold |
|
threshold.type |
|
verbose |
|
RC |
|
use.freq |
|
shuffle.k |
|
shuffle.method |
|
shuffle.leftovers |
|
return.scan.results |
|
progress |
|
BP |
|
To find enriched motifs, scan_sequences()
is run on both
target and background sequences. If search.mode = 'hits'
,
stats::fisher.test()
is run to test for enrichment. If
search.mode = 'positional'
, then the test as set by
positional.test
is run to check for positional differences
between target and background sequences. However if
positional.test = 'shapiro.test'
, then only target sequence
hits are considered.
data.frame
Motif enrichment results. The resulting
data.frame
contains the following columns:
* motif
Motif name.
* total.seq.hits
Total number of matches accross all target
sequences.
* num.seqs.hits
Number of target sequences which contain matches.
* num.seqs.total
Number of target sequences.
* total.bkg.hits
Total number of matches accross all background
sequences.
* num.bkg.hits
Number of background sequences which contain
matches.
* num.bkg.total
Number of background sequences.
* Pval.hits
P-value of enrichment. Only shown if
search.mode = c('hits', 'both')
.
* Qval.hits
Q-val of enrichment. Only shown if
search.mode = c('hits', 'both')
.
* Eval.hits
E-val of enrichment. Only shown if
search.mode = c('hits', 'both')
.
* Pval.pos
P-value of positional comparison. Only
shown if search.mode = c('positional', 'both')
.
* Qval.pos
Q-value of positional comparison. Only
shown if search.mode = c('positional', 'both')
.
* Eval.pos
E-value of positional comparison. Only
shown if search.mode = c('positional', 'both')
.
Benjamin Jean-Marie Tremblay b2tremblay@uwaterloo.ca
McLeay R, Bailey T (2010). “Motif Enrichment Analysis: A unified framework and method evaluation.” BMC Bioinformatics, 11.
scan_sequences()
, shuffle_sequences()
,
add_multifreq()
, motif_pvalue()
data(ArabidopsisPromoters) data(ArabidopsisMotif) enrich_motifs(ArabidopsisMotif, ArabidopsisPromoters, threshold = 0.01)