similarityMatrix: Similarity score matrix

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

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)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.