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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/repoverlap.R
\name{repOverlap}
\alias{repOverlap}
\title{General function for the repertoire overlap evaluation.}
\usage{
repOverlap(
.data,
.method = c("exact", "hamm", "lev", "jaccard", "morisita", "tversky", "overlap",
"horn"),
.seq = c("nuc", "aa"),
.quant = c("read.count", "umi.count", "read.prop", "umi.prop"),
.vgene = F,
.norm = T,
.a = 0.5,
.b = 0.5,
.do.unique = T,
.verbose = T
)
}
\arguments{
\item{.data}{List of clonesets.}
\item{.method}{Which method to use for the overlap evaluation. See "Details" for methods.}
\item{.seq}{Which clonotype sequences to use for the overlap: "nuc" for "CDR3.nucleotide.sequence", "aa" for
"CDR3.amino.acid.sequence".}
\item{.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".}
\item{.vgene}{If T than use V genes in computing shared or similar clonotypes. Used in all methods.}
\item{.norm}{If T than compute the normalised number of shared clonotypes. Used in "exact".}
\item{.a, .b}{Alpha and beta parameters for "tversky". Default values gives the Jaccard index measure.}
\item{.do.unique}{If T than remove duplicates from the input data, but add their quantities to their clones.}
\item{.verbose}{If T than output the data processing progress bar.}
}
\description{
General interface to all cloneset overlap functions.
}
\details{
You can see a more detailed description for each overlap method at \link{intersectClonesets} and \link{similarity}.
Parameter \code{.method} can have one of the following value each corresponding to the specific method:
- "exact" for the shared number of clonotypes (basic function \code{intersectClonesets(..., .type = "..e")}).
- "hamm" for the number of similar clonotypes by the Hamming distance (basic function \code{intersectClonesets(..., .type = "..h")}).
- "lev" for the number of similar clonotypes by the Levenshtein distance (basic function \code{intersectClonesets(..., .type = "..l")}).
- "jaccard" for the Jaccard index (basic function \code{jaccard.index}).
- "morisita" for the Morisita's overlap index (basic function \code{morisita.index}).
- "tversky" for the Tversky index (basic function \code{tversky.index}).
- "overlap" for the overlap coefficient (basic function \code{overlap.coef}).
- "horn" for the Horn's index (basic function \code{horn.index}).
}
\examples{
\dontrun{
data(twb)
repOverlap(twb, "exact", .seq = "nuc", .vgene = F)
repOverlap(twb, "morisita", .seq = "aa", .vgene = T, .quant = "umi.count")
ov <- repOverlap(twb)
ov[is.na(ov)] <- 0
vis.pca(prcomp(ov, scale. = T), list(A = c(1, 2), B = c(3, 4)))
}
}
\seealso{
\link{intersectClonesets}, \link{similarity}, \link{repDiversity}
}
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