similarityMatrix {LymphoSeq} | R Documentation

## Similarity score matrix

### Description

Calculates the similarity score of all pairwise comparison from a list of data frames.

### Usage

    similarityMatrix(productive.seqs)

### Arguments

`productive.seqs` | A list data frames of productive sequences generated by the LymphoSeq function productiveSeq. "count" and "aminoAcid" are a required columns.

### Value

A data frame of similarity scores calculated from all pairwise comparisons. The similarity scores is a measure of the amount of overlap between two samples. The value ranges from 0 to 1 where 1 indicates the sequence frequencies are identical in the two samples and 0 indicates no shared frequencies.

### See Also

`pairwisePlot` for plotting results as a heat map.

### Examples

    file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

    file.list <- readImmunoSeq(path = file.path)

    productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

    similarityMatrix(productive.seqs = productive.aa)

[Package LymphoSeq version 1.12.0 Index]