bhattacharyyaMatrix: Bhattacharyya matrix
In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors
Description
Usage
Arguments
Value
See Also
Examples
View source: R/bhattacharyyaMatrix.R
Description
Calculates the Bhattacharyya coefficient of all pairwise comparison from a
list of data frames.
Usage
1
bhattacharyyaMatrix(productive.seqs)
Arguments
productive.seqs
A list data frames of productive sequences generated
by the LymphoSeq function productiveSeq. "frequencyCount" and "aminoAcid"
are a required columns.
Value
A 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
pairwisePlot for plotting results as a heat map.
Examples
1
2
3
4
5
6
7
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)
Example output
Loading required package: LymphoSeqDB
Registered S3 method overwritten by 'treeio':
method from
root.phylo ape
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.
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TRB_Unsorted_1496 TRB_Unsorted_1320 TRB_Unsorted_949
TRB_Unsorted_1496 1.00000000 0.95291865 0.85590946
TRB_Unsorted_1320 0.95291865 1.00000000 0.87674297
TRB_Unsorted_949 0.85590946 0.87674297 1.00000000
TRB_Unsorted_369 0.52401899 0.53276440 0.51749643
TRB_Unsorted_83 0.30375115 0.33141730 0.37518862
TRB_Unsorted_32 0.28782025 0.31292611 0.28018709
TRB_CD8_CMV_369 0.75528817 0.77886610 0.71503376
TRB_Unsorted_0 0.01542965 0.01627338 0.01388704
TRB_CD8_949 0.78871302 0.81794347 0.81414832
TRB_CD4_949 0.44361207 0.43743309 0.42587691
TRB_Unsorted_369 TRB_Unsorted_83 TRB_Unsorted_32
TRB_Unsorted_1496 0.524018989 0.30375115 0.287820253
TRB_Unsorted_1320 0.532764399 0.33141730 0.312926108
TRB_Unsorted_949 0.517496433 0.37518862 0.280187090
TRB_Unsorted_369 1.000000000 0.46978757 0.192342747
TRB_Unsorted_83 0.469787569 1.00000000 0.297865580
TRB_Unsorted_32 0.192342747 0.29786558 1.000000000
TRB_CD8_CMV_369 0.512020867 0.40059194 0.272207037
TRB_Unsorted_0 0.008900138 0.01347907 0.008658058
TRB_CD8_949 0.532143928 0.43208064 0.350967319
TRB_CD4_949 0.176016728 0.06449128 0.023973222
TRB_CD8_CMV_369 TRB_Unsorted_0 TRB_CD8_949 TRB_CD4_949
TRB_Unsorted_1496 0.755288167 0.015429649 0.78871302 0.443612066
TRB_Unsorted_1320 0.778866101 0.016273376 0.81794347 0.437433093
TRB_Unsorted_949 0.715033758 0.013887037 0.81414832 0.425876907
TRB_Unsorted_369 0.512020867 0.008900138 0.53214393 0.176016728
TRB_Unsorted_83 0.400591940 0.013479071 0.43208064 0.064491279
TRB_Unsorted_32 0.272207037 0.008658058 0.35096732 0.023973222
TRB_CD8_CMV_369 1.000000000 0.008967238 0.86559885 0.001116121
TRB_Unsorted_0 0.008967238 1.000000000 0.04164991 0.006956798
TRB_CD8_949 0.865598846 0.041649912 1.00000000 0.000000000
TRB_CD4_949 0.001116121 0.006956798 0.00000000 1.000000000
LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.
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Description Usage Arguments Value See Also Examples
View source: R/bhattacharyyaMatrix.R
Description
Calculates the Bhattacharyya coefficient of all pairwise comparison from a list of data frames.
Usage
1 | bhattacharyyaMatrix(productive.seqs)
|
Arguments
productive.seqs |
A list data frames of productive sequences generated by the LymphoSeq function productiveSeq. "frequencyCount" and "aminoAcid" are a required columns. |
Value
A 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
pairwisePlot for plotting results as a heat map.
Examples
1 2 3 4 5 6 7 | 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)
|
Example output
Loading required package: LymphoSeqDB
Registered S3 method overwritten by 'treeio':
method from
root.phylo ape
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.
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TRB_Unsorted_1496 TRB_Unsorted_1320 TRB_Unsorted_949
TRB_Unsorted_1496 1.00000000 0.95291865 0.85590946
TRB_Unsorted_1320 0.95291865 1.00000000 0.87674297
TRB_Unsorted_949 0.85590946 0.87674297 1.00000000
TRB_Unsorted_369 0.52401899 0.53276440 0.51749643
TRB_Unsorted_83 0.30375115 0.33141730 0.37518862
TRB_Unsorted_32 0.28782025 0.31292611 0.28018709
TRB_CD8_CMV_369 0.75528817 0.77886610 0.71503376
TRB_Unsorted_0 0.01542965 0.01627338 0.01388704
TRB_CD8_949 0.78871302 0.81794347 0.81414832
TRB_CD4_949 0.44361207 0.43743309 0.42587691
TRB_Unsorted_369 TRB_Unsorted_83 TRB_Unsorted_32
TRB_Unsorted_1496 0.524018989 0.30375115 0.287820253
TRB_Unsorted_1320 0.532764399 0.33141730 0.312926108
TRB_Unsorted_949 0.517496433 0.37518862 0.280187090
TRB_Unsorted_369 1.000000000 0.46978757 0.192342747
TRB_Unsorted_83 0.469787569 1.00000000 0.297865580
TRB_Unsorted_32 0.192342747 0.29786558 1.000000000
TRB_CD8_CMV_369 0.512020867 0.40059194 0.272207037
TRB_Unsorted_0 0.008900138 0.01347907 0.008658058
TRB_CD8_949 0.532143928 0.43208064 0.350967319
TRB_CD4_949 0.176016728 0.06449128 0.023973222
TRB_CD8_CMV_369 TRB_Unsorted_0 TRB_CD8_949 TRB_CD4_949
TRB_Unsorted_1496 0.755288167 0.015429649 0.78871302 0.443612066
TRB_Unsorted_1320 0.778866101 0.016273376 0.81794347 0.437433093
TRB_Unsorted_949 0.715033758 0.013887037 0.81414832 0.425876907
TRB_Unsorted_369 0.512020867 0.008900138 0.53214393 0.176016728
TRB_Unsorted_83 0.400591940 0.013479071 0.43208064 0.064491279
TRB_Unsorted_32 0.272207037 0.008658058 0.35096732 0.023973222
TRB_CD8_CMV_369 1.000000000 0.008967238 0.86559885 0.001116121
TRB_Unsorted_0 0.008967238 1.000000000 0.04164991 0.006956798
TRB_CD8_949 0.865598846 0.041649912 1.00000000 0.000000000
TRB_CD4_949 0.001116121 0.006956798 0.00000000 1.000000000
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