Description Usage Arguments Details Value Author(s) References See Also Examples
This function calculates different dissmilarity/distance indices of sequences.
1 2 3 | sequences.distance(sequences = NULL, groups = NULL,
method = c("levenshtein", "cosine", "q-gram", "jaccard", "ja-wi",
"dam-le", "hamming", "osa", "lcs"), divLength = FALSE)
|
sequences |
Vector containing sequences |
groups |
Vector containing names of different samples (if present) |
method |
Dissmilariy method (see details) |
divLength |
Divide sequences into subsets of the same sequence length? (default: FALSE) |
This function calculates dissmiliarity/distance indices based on sequences. Levenshtein, cosine, q-gram, Jaccard, Jaro-Winker (ja-wi
), Damerau-Levenshtein (dam-le
), Hamming, Optimal string alignment (osa
) and longest common substring (lcs
) distance can be chosen. For details see stringdist-metrics
.
Output is a distance matrix containing dissimilarity indices/distances between sequences.
Julia Bischof
van der Loo M (2014). The stringdist package for approximate string matching. The R Journal, 6, pp. 111-122. https://CRAN.R-project.org/package=stringdist
dist.PCoA
, plotDistPCoA
, geneUsage.distance
1 2 3 4 5 6 7 8 9 | ## Not run:
data(clones.ind)
data(clones.allind)
dist1<-sequences.distance(sequences = clones.ind$unique_CDR3_sequences_AA,
method = "levenshtein", divLength=TRUE)
dist2<-sequences.distance(sequences = clones.allind$unique_CDR3_sequences_AA,
groups = clones.allind$individuals, method = "cosine", divLength=FALSE)
## End(Not run)
|
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