similarityMatrix: Similarity score matrix

Description Usage Arguments Value See Also Examples

View source: R/similarityMatrix.R

Description

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

Usage

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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

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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)

LymphoSeq documentation built on Nov. 1, 2018, 3:54 a.m.