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Last data update: 2014.03.03 |
Bhattacharyya matrixDescriptionCalculates the Bhattacharyya coefficient of all pairwise comparison from a list of data frames. UsagebhattacharyyaMatrix(productive.seqs) Arguments
ValueA data frame of Bhattacharyya coefficients calculated from all pairwise comparisons from a list of sample data frames. The Bhattacharyya coefficient 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
Examples
file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
file.list <- readImmunoSeq(path = file.path)
productive.aa <- productiveSeq(file.list, aggregate = "aminoAcid")
bhattacharyyaMatrix(productive.seqs = productive.aa)
Results
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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/bhattacharyyaMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bhattacharyyaMatrix
> ### Title: Bhattacharyya matrix
> ### Aliases: bhattacharyyaMatrix
>
> ### ** 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%
>
> bhattacharyyaMatrix(productive.seqs = productive.aa)
TCRB_Day1320_Unsorted TCRB_Day949_Unsorted
TCRB_Day1320_Unsorted 1.00000000 0.88013589
TCRB_Day949_Unsorted 0.88013589 1.00000000
TCRB_Day369_Unsorted 0.84210238 0.77225070
TCRB_Day1320_CD8_CMV 0.46204244 0.39421126
TCRB_Day83_Unsorted 0.62582845 0.58334619
TCRB_Day369_CD8_CMV 0.79605192 0.72972153
TCRB_Day32_Unsorted 0.32118959 0.27850843
TCRB_Day83_CD8_CMV 0.42168018 0.40854427
TCRB_Day0_Unsorted 0.01700697 0.01416233
TCRB_Day949_CD8 0.81836252 0.81470456
TCRB_Day949_CD4 0.44279429 0.42687836
TCRB_Day369_Unsorted TCRB_Day1320_CD8_CMV
TCRB_Day1320_Unsorted 0.84210238 0.462042437
TCRB_Day949_Unsorted 0.77225070 0.394211257
TCRB_Day369_Unsorted 1.00000000 0.435165772
TCRB_Day1320_CD8_CMV 0.43516577 1.000000000
TCRB_Day83_Unsorted 0.67953684 0.295356983
TCRB_Day369_CD8_CMV 0.82116105 0.482124408
TCRB_Day32_Unsorted 0.29995125 0.082152082
TCRB_Day83_CD8_CMV 0.44969014 0.113824462
TCRB_Day0_Unsorted 0.02196738 0.005328006
TCRB_Day949_CD8 0.78877245 0.473735619
TCRB_Day949_CD4 0.25231726 0.000000000
TCRB_Day83_Unsorted TCRB_Day369_CD8_CMV
TCRB_Day1320_Unsorted 0.62582845 0.7960519242
TCRB_Day949_Unsorted 0.58334619 0.7297215291
TCRB_Day369_Unsorted 0.67953684 0.8211610507
TCRB_Day1320_CD8_CMV 0.29535698 0.4821244077
TCRB_Day83_Unsorted 1.00000000 0.7060852420
TCRB_Day369_CD8_CMV 0.70608524 1.0000000000
TCRB_Day32_Unsorted 0.34304097 0.2754388006
TCRB_Day83_CD8_CMV 0.50422265 0.5072677597
TCRB_Day0_Unsorted 0.01058337 0.0088291544
TCRB_Day949_CD8 0.70092154 0.8841136749
TCRB_Day949_CD4 0.06984370 0.0007011302
TCRB_Day32_Unsorted TCRB_Day83_CD8_CMV TCRB_Day0_Unsorted
TCRB_Day1320_Unsorted 0.321189585 0.42168018 0.017006967
TCRB_Day949_Unsorted 0.278508431 0.40854427 0.014162333
TCRB_Day369_Unsorted 0.299951246 0.44969014 0.021967375
TCRB_Day1320_CD8_CMV 0.082152082 0.11382446 0.005328006
TCRB_Day83_Unsorted 0.343040971 0.50422265 0.010583367
TCRB_Day369_CD8_CMV 0.275438801 0.50726776 0.008829154
TCRB_Day32_Unsorted 1.000000000 0.14433344 0.008706795
TCRB_Day83_CD8_CMV 0.144333442 1.00000000 0.034586943
TCRB_Day0_Unsorted 0.008706795 0.03458694 1.000000000
TCRB_Day949_CD8 0.350076032 0.49596590 0.042637306
TCRB_Day949_CD4 0.024451859 0.00000000 0.006903870
TCRB_Day949_CD8 TCRB_Day949_CD4
TCRB_Day1320_Unsorted 0.81836252 0.4427942871
TCRB_Day949_Unsorted 0.81470456 0.4268783551
TCRB_Day369_Unsorted 0.78877245 0.2523172648
TCRB_Day1320_CD8_CMV 0.47373562 0.0000000000
TCRB_Day83_Unsorted 0.70092154 0.0698437032
TCRB_Day369_CD8_CMV 0.88411367 0.0007011302
TCRB_Day32_Unsorted 0.35007603 0.0244518587
TCRB_Day83_CD8_CMV 0.49596590 0.0000000000
TCRB_Day0_Unsorted 0.04263731 0.0069038699
TCRB_Day949_CD8 1.00000000 0.0000000000
TCRB_Day949_CD4 0.00000000 1.0000000000
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> dev.off()
null device
1
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