View source: R/motif_enrichment_multi_promotor_seqs.R
motif_enrichment_multi_promotor_seqs | R Documentation |
Compare the number of motifs in a set of non-random versus randomly sampled gene promotor sequences within a set of subject genomes. The resulting values are then used to statistically assess the enrichment of certain motifs in real sequences compared to randomly sampled gene promotor sequences.
motif_enrichment_multi_promotor_seqs(
blast_tbl,
subject_genomes,
annotation_files,
annotation_format = "gff",
test = "fisher",
alternative = "two.sided",
interval_width,
motifs,
max.mismatch = 0,
min.mismatch = 0,
...
)
blast_tbl |
a blast_table. |
subject_genomes |
a character vector storing the file paths to the subject genomes that shall be used as subject references. |
annotation_files |
a character vector storing the file paths to the subject annotation files in |
annotation_format |
the annotation format. Options are:
|
test |
|
alternative |
indicates the alternative hypothesis and must be one of |
interval_width |
total number of sequences that shall be sampled per subject genome. |
motifs |
a character vector storing (case sensitive) motif sequences for which abundance in the sampled sequences shall be assessed. |
max.mismatch |
maximum number of mismatches that are allowed between the sequence motif and the matching region in the sampled sequence. |
min.mismatch |
minimum number of mismatches that are allowed between the sequence motif and the matching region in the sampled sequence. |
... |
additional arguments passed to |
Hajk-Georg Drost
motif_count
, motif_compare_multi_promotor_seqs
, motif_compare
,
motif_enrichment
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