Description Usage Arguments Details Value See Also Examples
This function is a wrapper that will detect and either remove or 'fix' hypermutated sequences depending of the value of the 'fix_with' argument.
remove_hypermut(dat, verbose = TRUE, fix_with = FALSE, ancestor = "consensus", p_value = 0.05)
The sequence data. The structure must match the format produced
by read.fasta from the seqinr package. This is a list in which each element
represents a single sequence. Each element is of class
If TRUE, print the name and p-value of removed/fixed sequences.
Either FALSE or a single letter. If not FALSE, then replace the hypermutated base with the letter indicated.
Either 'consensus' to indicate that the consensus sequences must be computed, or 'first' to indicate that the first sequence in the dataset should be considered to be the ancestral sequence, or the ancestral sequence itself.
The p-value used by the one-sided fischer test.
ancestor_processing to obtain the ancestral sequence to
compare the query sequences to, then calls
deduplicate_seqs to remove
duplicate sequences for performance reasons, next loops over each unique
sequence, comparing it to the ancestral sequence with
finally collates the results.
A list with three elements:
A data.frame that contains all the positions in all the sequences that are either a hypermutation or control position.
A list that stores all the sequences that did not contain any hypermutation and, in the case that the fix_with parameter was set, those sequences with hypermutation that was corrected.
A list of all the sequences that contains hypermutation.
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result <- remove_hypermut(hd_seqs) names(result) str(result)
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