percentSI: Percent similarity index

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Percent similarity index

Description

Calculates the Percent similarity index between two groups of repertoires. Percent similarity index, not only compares the number of similar and dissimilar species present between two sites, but also incorporate abundance.

Usage

percentSI(sample_list)

Arguments

sample_list

A list of two tibble corresponding derived from the productiveSeq() function in LymphoSeq2. "duplicate_frequency", "junction_aa", and "repertoire_id" columns are necessary for the calculation of the Bhattacharyya coefficient.

Value

Returns the similarity score, 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

scoringMatrix()

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.