# General function for the repertoire overlap evaluation.

### Description

General interface to all cloneset overlap functions.

### Usage

1 2 3 4 5 |

### Arguments

`.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. |

### Details

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`

).

### See Also

intersectClonesets, similarity, repDiversity

### Examples

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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