Bhattacharyya coefficient

Description

Calculates the Bhattacharyya coefficient of two samples.

Usage

bhattacharyyaCoefficient(sample1, sample2)

Arguments

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[["TCRB_Day32_Unsorted"]], 
   productive.aa[["TCRB_Day83_Unsorted"]])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/bhattacharyyaCoefficient.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bhattacharyyaCoefficient
> ### Title: Bhattacharyya coefficient
> ### Aliases: bhattacharyyaCoefficient
> 
> ### ** Examples
> 
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
> 
> file.list <- readImmunoSeq(path = file.path)
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> productive.aa <- productiveSeq(file.list, aggregate = "aminoAcid")
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> bhattacharyyaCoefficient(productive.aa[["TCRB_Day32_Unsorted"]], 
+    productive.aa[["TCRB_Day83_Unsorted"]])
[1] 0.343041
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>