This function assesses pairwise repertoire dissimilarities using a specific dissimilarity method.
It calculates a list of dissimilarity indices, each taking into account different parameters. The proposed methods include:
The Jaccard similarity: a measure of similarity between sample sets defined as the size of the intersection divided by the size of the union of the sample sets.
The Morisita-Horn similarity: a measure of similarity that tends to be over-sensitive to abundant species.
Usage
CalcDissimilarity(
x,
level = c("aaClone", "ntClone", "V", "J", "VJ", "ntCDR3", "aaCDR3"),
method = c("manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski",
"jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial",
"chao", "cao", "mahalanobis"),
binary = FALSE
)Arguments
- x
an object of class
RepSeqExperiment- level
a character specifying the level of the repertoire on which the indices are computed. Should be one of "aaClone","ntClone", "V", "J", "VJ", "ntCDR3" or "aaCDR3".
- method
a character specifying the distance method to be computed. Should be one of the following: "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis."
- binary
a boolean indicating whether or not to transform the data into a presence/absence data. Default is FALSE
Details
Details on the calculated indices can be found in the vegan package: https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/vegdist
Examples
CalcDissimilarity(x = RepSeqData,
level = "V", method = "jaccard" )
#> tripod-30-813 tripod-30-815 tripod-31-846 tripod-31-848
#> tripod-30-813 0.0000000 0.33363625 0.5463870 0.35924955
#> tripod-30-815 0.3336363 0.00000000 0.3250372 0.07883753
#> tripod-31-846 0.5463870 0.32503723 0.0000000 0.30055411
#> tripod-31-848 0.3592496 0.07883753 0.3005541 0.00000000
#> tripod-35-970 0.5862839 0.38544553 0.1678604 0.36615773
#> tripod-35-972 0.5933492 0.39541961 0.2107167 0.37323187
#> tripod-36-1003 0.4719296 0.21541907 0.1899473 0.19943418
#> tripod-36-1005 0.6597488 0.49391196 0.2687513 0.47486503
#> tripod-35-970 tripod-35-972 tripod-36-1003 tripod-36-1005
#> tripod-30-813 0.5862839 0.5933492 0.4719296 0.6597488
#> tripod-30-815 0.3854455 0.3954196 0.2154191 0.4939120
#> tripod-31-846 0.1678604 0.2107167 0.1899473 0.2687513
#> tripod-31-848 0.3661577 0.3732319 0.1994342 0.4748650
#> tripod-35-970 0.0000000 0.2432651 0.2628019 0.2191123
#> tripod-35-972 0.2432651 0.0000000 0.2485693 0.2585902
#> tripod-36-1003 0.2628019 0.2485693 0.0000000 0.3601864
#> tripod-36-1005 0.2191123 0.2585902 0.3601864 0.0000000