motif_compare_multi: Count the number of motifs in a set of non-random versus...

In HajkD/metablastr: Perform Massive Local BLAST Searches

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

Description

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.

Usage

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(s)

Hajk-Georg Drost

See Also

motif_count, motif_compare_multi_promotor_seqs, motif_compare, motif_enrichment, motif_enrichment_multi

HajkD/metablastr documentation built on Sept. 14, 2023, 5:26 p.m.