dot-filterSeqs: Filter Sequences

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Filter Sequences

Description

Filter sequences that are unlikely to be useful for motif enrichment analysis. The current defaults are based on HOMER (version 4.11).

Usage

.filterSeqs(
  seqs,
  maxFracN = 0.7,
  minLength = 5L,
  maxLength = 100000L,
  verbose = FALSE
)

Arguments

seqs	a DNAStringSet object.
maxFracN	A numeric scalar with the maximal fraction of N bases allowed in a sequence (defaults to 0.7).
minLength	The minimum sequence length (default from Homer). Sequences shorter than this will be filtered out.
maxLength	The maximum sequence length (default from Homer). Sequences bigger than this will be filtered out.
verbose	A logical scalar. If TRUE, report on filtering.

Details

The filtering logic is based on removePoorSeq.pl from Homer.

Value

a logical vector of the same length as seqs with TRUE indicated to keep the sequence and FALSE to filter it out.

fmicompbio/monaLisa documentation built on July 10, 2024, 8:44 a.m.