enrich_motifs_fisher: Function to clean up .meme motif files. Remove duplicate...

In TedCCLeung/PhotoperiodMotif: What the Package Does (One Line, Title Case)

Function to clean up .meme motif files. Remove duplicate names if there is any. Remove duplicate motifs if there is any.

Description

Function to clean up .meme motif files. Remove duplicate names if there is any. Remove duplicate motifs if there is any.

Usage

enrich_motifs_fisher(
  qry_gff3,
  bkg_gff3,
  qry_fa,
  bkg_fa,
  alternative = "two.sided",
  motif_max_p = 1e-05
)

Arguments

qry_gff3	Character vector of file paths of .gff3 files to be mapped on.
bkg_gff3	Character vector of file paths of .gff3 files to be used as background.
qry_fa	Character vector of file paths of .fa files to be mapped on.
bkg_fa	Character vector of file paths of .fa files to be used as background.
alternative	Character. Alternative hypothesis of the Fisher's test from the stats package.
motif_max_p	Numerical. What value of p value to cap if very low p values were encountered.

Value

Data frame of the p value and fold enrichment.

TedCCLeung/PhotoperiodMotif documentation built on April 27, 2022, 9:01 p.m.