scoringMatrix: Bhattacharyya, Similarity, Sorensen, or PSI matrix

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Bhattacharyya, Similarity, Sorensen, or PSI matrix

Description

Calculates the Bhattacharyya coefficient, Similarity score, Sorensen Index, or Percent Similarity Index of all pairwise comparison from a list of data frames.

Usage

scoringMatrix(productive_table, mode = "Bhattacharyya")

Arguments

productive_table	A tibble of productive sequences generated by the LymphoSeq function productiveSeq. "duplicate_frequency" and "junction_aa" are a required columns.
mode	The mode to use for calculating pairwise similarity. Can take the values "Bhattacharyya", "Similarity", "Sorensen", or "PSI". Default is "Bhattacharyya".

Value

A data frame of Bhattacharyya coefficients, Similarity scores, Sorensen Index, or Percent Similarity Index calculated from all pairwise comparisons from a list of repertoire_id data frames. Both metrics measure 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.

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.