View source: R/motif_enrichment.R
motif_enrichment | R Documentation |
Compare the number of motifs in a set of non-random versus random sequences. The resulting values are then tested for enrichment of certain motifs in real sequences compared to random sequences. Several tests statistics and approaches are available to quantify significant motif enrichment.
motif_enrichment(
real_seqs,
random_seqs,
motifs,
test = "fisher",
alternative = "less",
max.mismatch = 0,
min.mismatch = 0,
...
)
real_seqs |
a file path to the |
random_seqs |
a file path to the |
motifs |
a character vector storing a set of motifs that shall be counted within respective sequences. |
test |
tests statistics and models to quantify significant motif enrichment. Options are:
|
alternative |
indicates the alternative hypothesis and must be one of |
max.mismatch |
the maximum number of mismatching letters allowed (see |
min.mismatch |
the minimum number of mismatching letters allowed (see |
... |
additional arguments passed to |
Hajk-Georg Drost
motif_count
, extract_random_seqs_from_genome
, extract_hit_seqs_from_genomes
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