.defineBackground {monaLisa} | R Documentation |
Define the background set for the motif enrichment calculation in a single bin, depending on the background mode and given foreground sequences.
.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) )
sqs, bns, bg |
The |
currbn |
An |
gnm, gnm.regions, gnm.oversample |
The |
maxFracN |
The |
GCbreaks |
The breaks between GC bins. The default value is based on the hard-coded bins used in Homer. |
a DataFrame
with sequences represented by rows and columns
seqs
, isForeground
, GCfrac
, GCbin
, GCwgt
and seqWgt
. Only the first three are already filled in.