.normForKmers {monaLisa} | R Documentation |
Adjust background sequence weights for differences in k-mer
composition compared to the foreground sequences. This function
implements a single iteration, and is called iteratively by
.iterativeNormForKmers
to get to the final set of adjusted
weights, which will be the result of adjusting for GC and k-mer
composition. The logic is based on Homer's
normalizeSequenceIteration()
function found in Motif2.cpp
.
.normForKmers( kmerFreq, goodKmers, kmerRC, seqWgt, isForeground, minSeqWgt = 0.001, maxSeqWgt = 1000 )
kmerFreq |
a |
goodKmers |
a |
kmerRC |
a |
seqWgt |
a |
isForeground |
logical vector of the same length as |
minSeqWgt |
Numeric scalar greater than zero giving the
minimal weight of a sequence. The default value (0.001) is based on
|
maxSeqWgt |
Numeric scalar greater than zero giving the
maximal weight of a sequence. The default value (1000) is based on
|
a named list
with elements seqWgt
(updated
weights) and err
(error measuring difference of foreground
and weighted background sequence compositions).