bhattacharyyaCoefficient: Bhattacharyya coefficient

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

Description

Calculates the Bhattacharyya coefficient of two samples.

Usage

bhattacharyyaCoefficient(sample1, sample2)

Arguments

sample1	A data frame consisting of frequencies of antigen receptor sequences. "frequencyCount" is a required column.
sample2	A data frame consisting of frequencies of antigen receptor sequences. "frequencyCount" is a required column.

Value

Returns the Bhattacharyya coefficient, 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

bhattacharyyaMatrix

Examples

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

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

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

bhattacharyyaCoefficient(productive.aa[["TRB_Unsorted_32"]], 
   productive.aa[["TRB_Unsorted_83"]])

Example output

Loading required package: LymphoSeqDB
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.

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[1] 0.2978656

LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.