Count the number of motifs in a set of non-random versus randomly sampled genomic sequences for multiple species

Source: R/motif_compare_multi.R

Compare the number of motifs in a set of non-random versus random sequences within a set of subject genomes. The resulting values can then be used to test the enrichment of certain motifs in real sequences compared to random sequences. Each enrichment analysis is performed for a set of different species or genomes.

motif_compare_multi(
  blast_tbl,
  subject_genomes,
  size,
  interval_width,
  motifs,
  max.mismatch = 0,
  min.mismatch = 0,
  ...
)

Arguments

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.

size

total number of sequences that shall be sampled per subject genome.

interval_width

length of the sequence in which motifs shall be detected.

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 motif_compare.

Author

Hajk-Georg Drost