General interface to all cloneset overlap functions.
1 2 3 4 5 
.data 
List of clonesets. 
.method 
Which method to use for the overlap evaluation. See "Details" for methods. 
.seq 
Which clonotype sequences to use for the overlap: "nuc" for "CDR3.nucleotide.sequence", "aa" for "CDR3.amino.acid.sequence". 
.quant 
Which column to use for the quantity of clonotypes: "read.count" for the "Read.count" column, "umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.prop" for the "Umi.proportion" column. Used in "morisita" and "horn". 
.vgene 
If T than use V genes in computing shared or similar clonotypes. Used in all methods. 
.norm 
If T than compute the normalised number of shared clonotypes. Used in "exact". 
.a, .b 
Alpha and beta parameters for "tversky". Default values gives the Jaccard index measure. 
.do.unique 
If T than remove duplicates from the input data, but add their quantities to their clones. 
.verbose 
If T than output the data processing progress bar. 
You can see a more detailed description for each overlap method at intersectClonesets and similarity.
Parameter .method
can have one of the following value each corresponding to the specific method:
 "exact" for the shared number of clonotypes (basic function intersectClonesets(..., .type = "..e")
).
 "hamm" for the number of similar clonotypes by the Hamming distance (basic function intersectClonesets(..., .type = "..h")
).
 "lev" for the number of similar clonotypes by the Levenshtein distance (basic function intersectClonesets(..., .type = "..l")
).
 "jaccard" for the Jaccard index (basic function jaccard.index
).
 "morisita" for the Morisita's overlap index (basic function morisita.index
).
 "tversky" for the Tversky index (basic function tversky.index
).
 "overlap" for the overlap coefficient (basic function overlap.coef
).
 "horn" for the Horn's index (basic function horn.index
).
intersectClonesets, similarity, repDiversity
1 2 3 4 5 6 7 8  ## Not run:
data(twb)
repOverlap(twb, "exact", .seq = "nuc", .vgene = F)
repOverlap(twb, "morisita", .seq = "aa", .vgene = T, .quant = "umi.count")
ov < repOverlap(twb)
vis.pca(prcomp(ov, scale. = T), list(A = c(1, 2), B = c(3, 4)))
## End(Not run)

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