check_N: Check proportion of N bases in each sequence.
In ClassifyITS: Fungal Assignment Pipeline
check_N R Documentation
Check proportion of N bases in each sequence.
Description
Calculates the proportion of "N" bases (ambiguous bases) in each sequence and flags if above the given threshold.
Usage
check_N(rep_seqs, cutoff = 1)
Arguments
rep_seqs
Character vector, list (e.g., from seqinr::read.fasta(as.string=TRUE)),
or (optionally) a DNAStringSet.
cutoff
Numeric, percent threshold (default 1).
Value
Data frame with columns: qseqid, N_percent, N_flag.
Examples
seqs <- c(seq1 = "ATGCNNNN", seq2 = "NNNNATGC")
check_N(seqs)
check_N(seqs, cutoff = 10)
ClassifyITS documentation built on April 9, 2026, 5:08 p.m.
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| check_N | R Documentation |
Check proportion of N bases in each sequence.
Description
Calculates the proportion of "N" bases (ambiguous bases) in each sequence and flags if above the given threshold.
Usage
check_N(rep_seqs, cutoff = 1)
Arguments
rep_seqs |
Character vector, list (e.g., from seqinr::read.fasta(as.string=TRUE)), or (optionally) a DNAStringSet. |
cutoff |
Numeric, percent threshold (default 1). |
Value
Data frame with columns: qseqid, N_percent, N_flag.
Examples
seqs <- c(seq1 = "ATGCNNNN", seq2 = "NNNNATGC")
check_N(seqs)
check_N(seqs, cutoff = 10)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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