dot-defineBackground: Define background sequence set for a single motif enrichment...

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Define background sequence set for a single motif enrichment calculation

Description

Define the background set for the motif enrichment calculation in a single bin, depending on the background mode and given foreground sequences.

Usage

.defineBackground(
  sqs,
  bns,
  bg,
  currbn,
  gnm,
  gnm.regions,
  gnm.oversample,
  maxFracN = 0.7,
  GCbreaks = c(0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.6, 0.7, 0.8)
)

Arguments

sqs, bns, bg	The seqs, bins and background arguments from calcBinnedMotifEnrR.
currbn	An integer scalar with the current bin defining the foreground sequences.
gnm, gnm.regions, gnm.oversample	The genome, genome.regions and genome.oversample arguments from calcBinnedMotifEnrR.
maxFracN	The maxFracN argument from calcBinnedMotifEnrR.
GCbreaks	The breaks between GC bins. The default value is based on the hard-coded bins used in Homer.

Value

a DataFrame with sequences represented by rows and columns seqs, isForeground, GCfrac, GCbin, GCwgt and seqWgt. Only the first three are already filled in.

fmicompbio/monaLisa documentation built on Nov. 2, 2024, 1:33 p.m.