pairwiseEqual: Calculate pairwise equivalence between sequences
In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
pairwiseEqual R Documentation
Calculate pairwise equivalence between sequences
Description
pairwiseEqual determined pairwise equivalence between a pairs in a
set of sequences, excluding ambiguous positions (Ns and gaps).
Usage
pairwiseEqual(seq)
Arguments
seq
character vector containing a DNA sequences.
Value
A logical matrix of equivalence between each entry in seq.
Values are TRUE when sequences are equivalent and FALSE
when they are not.
See Also
Uses seqEqual for testing equivalence between pairs.
See pairwiseDist for generating a sequence distance matrix.
Examples
# Gaps and Ns will match any character
seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG")
d <- pairwiseEqual(seq)
rownames(d) <- colnames(d) <- seq
d
alakazam documentation built on Sept. 30, 2023, 9:07 a.m.
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| pairwiseEqual | R Documentation |
Calculate pairwise equivalence between sequences
Description
pairwiseEqual determined pairwise equivalence between a pairs in a
set of sequences, excluding ambiguous positions (Ns and gaps).
Usage
pairwiseEqual(seq)
Arguments
seq |
character vector containing a DNA sequences. |
Value
A logical matrix of equivalence between each entry in seq.
Values are TRUE when sequences are equivalent and FALSE
when they are not.
See Also
Uses seqEqual for testing equivalence between pairs. See pairwiseDist for generating a sequence distance matrix.
Examples
# Gaps and Ns will match any character
seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG")
d <- pairwiseEqual(seq)
rownames(d) <- colnames(d) <- seq
d
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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