searchPublished: Search for T cell receptor beta CDR3 amino acid sequences...
In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors
Description
Usage
Arguments
Value
See Also
Examples
View source: R/searchPublished.R
Description
Search for published T cell receptor beta CDR3 amino acid sequences with
known antigen specificity in a list of data frames.
Usage
1
Arguments
list
A list of data frames generated by the LymphoSeq functions
readImmunoSeq or productiveSeq. "aminoAcid", "frequencyCount", and "count"
are required columns.
Value
Returns a data frame of each sample name and instance in the sample
that the published TCR sequence appeared along with additional
information including antigen specificity, epitope, HLA type, and PubMed ID
(PMID) for the reference where the sequence was characterized. The
publishedTRB database is located in a separate package called LymphoSeqDB
that should be loaded automatically.
See Also
Refer to the LymphoSeqDB package for details regarding the
publishedTRB database.
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 = file.list, aggregate = "aminoAcid")
searchPublished(list = productive.aa)
Example output
Loading required package: LymphoSeqDB
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.
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sample aminoAcid count frequencyCount
1 TRB_Unsorted_32 CASASSGTDTQYF 33 0.131594688
2 TRB_Unsorted_1496 CASSETGGTEAFF 2 0.007267706
3 TRB_Unsorted_949 CASSFSTDTQYF 2 0.038277512
4 TRB_CD8_949 CASSIRSAYEQYF 7 0.031233268
5 TRB_Unsorted_1320 CASSIRSAYEQYF 15 0.010313886
6 TRB_Unsorted_1496 CASSIRSSYEQYF 4 0.014535412
7 TRB_Unsorted_32 CASSLAPSYEQYF 17 0.067791203
8 TRB_Unsorted_1320 CASSLGEQPQHF 10 0.006875924
9 TRB_Unsorted_1320 CASSPARNTEAFF 134 0.092137381
10 TRB_CD8_949 CASSPARNTEAFF 49 0.218632875
11 TRB_Unsorted_83 CASSPARNTEAFF 35 0.016896785
12 TRB_Unsorted_949 CASSPARNTEAFF 7 0.133971292
13 TRB_Unsorted_1496 CASSPARNTEAFF 23 0.083578618
14 TRB_CD8_CMV_369 CASSPARNTEAFF 15 1.005361930
15 TRB_CD8_949 CASSPHRNTEAFF 8 0.035695163
16 TRB_Unsorted_369 CASSPHRNTEAFF 72 0.025062395
17 TRB_Unsorted_949 CASSPHRNTEAFF 1 0.019138756
18 TRB_Unsorted_1320 CASSPHRNTEAFF 15 0.010313886
19 TRB_Unsorted_83 CASSPNRNTEAFF 369 0.178140388
20 TRB_CD8_949 CASSPNRNTEAFF 6 0.026771372
21 TRB_Unsorted_1496 CASSPQGLGTEAFF 4 0.014535412
22 TRB_Unsorted_0 CASSPQRNTEAFF 87 0.611040877
23 TRB_CD8_949 CASSPSRNTEAFF 106 0.472960914
24 TRB_Unsorted_1320 CASSPSRNTEAFF 210 0.144394403
25 TRB_Unsorted_1496 CASSPSRNTEAFF 42 0.152621825
26 TRB_Unsorted_83 CASSPSRNTEAFF 8376 4.043641981
27 TRB_CD8_CMV_369 CASSPSRNTEAFF 12 0.804289544
28 TRB_Unsorted_949 CASSPSRNTEAFF 13 0.248803828
29 TRB_Unsorted_1496 CASSQEGTGSYEQYF 1 0.003633853
30 TRB_CD8_949 CASSQGTGVSTEAFF 3 0.013385686
31 TRB_Unsorted_32 CASSRLAGGLDTQYF 9 0.035889460
32 TRB_Unsorted_369 CASSRTGITDTQYF 49 0.017056352
33 TRB_Unsorted_1496 CASSSTGGYTF 2 0.007267706
34 TRB_CD8_949 CASSVRSSYEQYF 2 0.008923791
35 TRB_Unsorted_0 CASSVSNQPQHF 1 0.007023458
36 TRB_Unsorted_1320 CASSYSGNTEAFF 103 0.070822017
37 TRB_CD8_CMV_369 CASSYSGNTEAFF 2 0.134048257
38 TRB_CD8_949 CASSYSGNTEAFF 38 0.169552026
39 TRB_Unsorted_369 CASSYSGNTEAFF 1118 0.389163299
40 TRB_Unsorted_1496 CASSYSGNTEAFF 21 0.076310912
41 TRB_Unsorted_949 CASSYSGNTEAFF 4 0.076555024
42 TRB_Unsorted_0 CASSYSGNTEAFF 6 0.042140750
43 TRB_Unsorted_83 CASSYSGNTEAFF 1737 0.838563291
estimatedNumberGenomes PMID HLA antigen epitope
1 0 20647322 HLA-A*24:02 Leukemia <NA>
2 2 19786555 HLA-A*02:01 Melanoma EAAGIGILTV
3 2 23267020 HLA-A*02 EBV BMFL1-GLCTLVAML
4 7 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
5 15 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
6 4 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
7 0 23267020 HLA-B*08 EBV BZLF1-RAKFKQLL
8 10 23521884 HLA-B*27:05 HIV KK10-KRWIILGLNK
9 134 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
10 49 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
11 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
12 7 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
13 23 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
14 15 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
15 8 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
16 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
17 1 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
18 15 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
19 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
20 6 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
21 4 19786555 HLA-A*02:01 Melanoma EAAGIGILTV
22 87 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
23 106 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
24 210 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
25 42 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
26 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
27 12 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
28 13 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
29 1 23267020 HLA-A*11 EBV EBNA3B-AVFDRKSDAK
30 3 12417573 HLA-A*02/HLA-B*08 HIV SLYNTVATL
31 0 25837513 HLA-A*02:01 Melanoma <NA>
32 0 25837513 HLA-A*02:01 Melanoma <NA>
33 2 24020931 <NA> CMV pp65
34 2 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
35 1 25837513 HLA-A*02:01 Melanoma <NA>
36 103 24020931 <NA> CMV pp65
37 2 24020931 <NA> CMV pp65
38 38 24020931 <NA> CMV pp65
39 0 24020931 <NA> CMV pp65
40 21 24020931 <NA> CMV pp65
41 4 24020931 <NA> CMV pp65
42 6 24020931 <NA> CMV pp65
43 0 24020931 <NA> CMV pp65
prevalence
1 7.3
2 34.5
3 85.5
4 18.2
5 18.2
6 45.5
7 69.1
8 29.1
9 47.3
10 47.3
11 47.3
12 47.3
13 47.3
14 47.3
15 30.9
16 30.9
17 30.9
18 30.9
19 43.6
20 43.6
21 21.8
22 69.1
23 65.5
24 65.5
25 65.5
26 65.5
27 65.5
28 65.5
29 34.5
30 7.3
31 29.1
32 25.5
33 29.1
34 36.4
35 52.7
36 69.1
37 69.1
38 69.1
39 69.1
40 69.1
41 69.1
42 69.1
43 69.1
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/searchPublished.R
Description
Search for published T cell receptor beta CDR3 amino acid sequences with known antigen specificity in a list of data frames.
Usage
1 |
Arguments
list |
A list of data frames generated by the LymphoSeq functions readImmunoSeq or productiveSeq. "aminoAcid", "frequencyCount", and "count" are required columns. |
Value
Returns a data frame of each sample name and instance in the sample that the published TCR sequence appeared along with additional information including antigen specificity, epitope, HLA type, and PubMed ID (PMID) for the reference where the sequence was characterized. The publishedTRB database is located in a separate package called LymphoSeqDB that should be loaded automatically.
See Also
Refer to the LymphoSeqDB package for details regarding the publishedTRB database.
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 = file.list, aggregate = "aminoAcid")
searchPublished(list = productive.aa)
|
Example output
Loading required package: LymphoSeqDB
sh: 1: cannot create /dev/null: Permission denied
Could not detect number of cores, defaulting to 1.
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|===================== | 30%
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|======================================================== | 80%
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|======================================================================| 100%
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|======================================================== | 80%
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|=============================================================== | 90%
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|======================================================================| 100%
sample aminoAcid count frequencyCount
1 TRB_Unsorted_32 CASASSGTDTQYF 33 0.131594688
2 TRB_Unsorted_1496 CASSETGGTEAFF 2 0.007267706
3 TRB_Unsorted_949 CASSFSTDTQYF 2 0.038277512
4 TRB_CD8_949 CASSIRSAYEQYF 7 0.031233268
5 TRB_Unsorted_1320 CASSIRSAYEQYF 15 0.010313886
6 TRB_Unsorted_1496 CASSIRSSYEQYF 4 0.014535412
7 TRB_Unsorted_32 CASSLAPSYEQYF 17 0.067791203
8 TRB_Unsorted_1320 CASSLGEQPQHF 10 0.006875924
9 TRB_Unsorted_1320 CASSPARNTEAFF 134 0.092137381
10 TRB_CD8_949 CASSPARNTEAFF 49 0.218632875
11 TRB_Unsorted_83 CASSPARNTEAFF 35 0.016896785
12 TRB_Unsorted_949 CASSPARNTEAFF 7 0.133971292
13 TRB_Unsorted_1496 CASSPARNTEAFF 23 0.083578618
14 TRB_CD8_CMV_369 CASSPARNTEAFF 15 1.005361930
15 TRB_CD8_949 CASSPHRNTEAFF 8 0.035695163
16 TRB_Unsorted_369 CASSPHRNTEAFF 72 0.025062395
17 TRB_Unsorted_949 CASSPHRNTEAFF 1 0.019138756
18 TRB_Unsorted_1320 CASSPHRNTEAFF 15 0.010313886
19 TRB_Unsorted_83 CASSPNRNTEAFF 369 0.178140388
20 TRB_CD8_949 CASSPNRNTEAFF 6 0.026771372
21 TRB_Unsorted_1496 CASSPQGLGTEAFF 4 0.014535412
22 TRB_Unsorted_0 CASSPQRNTEAFF 87 0.611040877
23 TRB_CD8_949 CASSPSRNTEAFF 106 0.472960914
24 TRB_Unsorted_1320 CASSPSRNTEAFF 210 0.144394403
25 TRB_Unsorted_1496 CASSPSRNTEAFF 42 0.152621825
26 TRB_Unsorted_83 CASSPSRNTEAFF 8376 4.043641981
27 TRB_CD8_CMV_369 CASSPSRNTEAFF 12 0.804289544
28 TRB_Unsorted_949 CASSPSRNTEAFF 13 0.248803828
29 TRB_Unsorted_1496 CASSQEGTGSYEQYF 1 0.003633853
30 TRB_CD8_949 CASSQGTGVSTEAFF 3 0.013385686
31 TRB_Unsorted_32 CASSRLAGGLDTQYF 9 0.035889460
32 TRB_Unsorted_369 CASSRTGITDTQYF 49 0.017056352
33 TRB_Unsorted_1496 CASSSTGGYTF 2 0.007267706
34 TRB_CD8_949 CASSVRSSYEQYF 2 0.008923791
35 TRB_Unsorted_0 CASSVSNQPQHF 1 0.007023458
36 TRB_Unsorted_1320 CASSYSGNTEAFF 103 0.070822017
37 TRB_CD8_CMV_369 CASSYSGNTEAFF 2 0.134048257
38 TRB_CD8_949 CASSYSGNTEAFF 38 0.169552026
39 TRB_Unsorted_369 CASSYSGNTEAFF 1118 0.389163299
40 TRB_Unsorted_1496 CASSYSGNTEAFF 21 0.076310912
41 TRB_Unsorted_949 CASSYSGNTEAFF 4 0.076555024
42 TRB_Unsorted_0 CASSYSGNTEAFF 6 0.042140750
43 TRB_Unsorted_83 CASSYSGNTEAFF 1737 0.838563291
estimatedNumberGenomes PMID HLA antigen epitope
1 0 20647322 HLA-A*24:02 Leukemia <NA>
2 2 19786555 HLA-A*02:01 Melanoma EAAGIGILTV
3 2 23267020 HLA-A*02 EBV BMFL1-GLCTLVAML
4 7 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
5 15 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
6 4 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
7 0 23267020 HLA-B*08 EBV BZLF1-RAKFKQLL
8 10 23521884 HLA-B*27:05 HIV KK10-KRWIILGLNK
9 134 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
10 49 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
11 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
12 7 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
13 23 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
14 15 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
15 8 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
16 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
17 1 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
18 15 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
19 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
20 6 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
21 4 19786555 HLA-A*02:01 Melanoma EAAGIGILTV
22 87 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
23 106 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
24 210 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
25 42 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
26 0 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
27 12 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
28 13 22323539 HLA-B*07 CMV pp65-RPHERNGFTVL
29 1 23267020 HLA-A*11 EBV EBNA3B-AVFDRKSDAK
30 3 12417573 HLA-A*02/HLA-B*08 HIV SLYNTVATL
31 0 25837513 HLA-A*02:01 Melanoma <NA>
32 0 25837513 HLA-A*02:01 Melanoma <NA>
33 2 24020931 <NA> CMV pp65
34 2 21048112 HLA-A*02 EBV BMLF1-GLCTLVAML
35 1 25837513 HLA-A*02:01 Melanoma <NA>
36 103 24020931 <NA> CMV pp65
37 2 24020931 <NA> CMV pp65
38 38 24020931 <NA> CMV pp65
39 0 24020931 <NA> CMV pp65
40 21 24020931 <NA> CMV pp65
41 4 24020931 <NA> CMV pp65
42 6 24020931 <NA> CMV pp65
43 0 24020931 <NA> CMV pp65
prevalence
1 7.3
2 34.5
3 85.5
4 18.2
5 18.2
6 45.5
7 69.1
8 29.1
9 47.3
10 47.3
11 47.3
12 47.3
13 47.3
14 47.3
15 30.9
16 30.9
17 30.9
18 30.9
19 43.6
20 43.6
21 21.8
22 69.1
23 65.5
24 65.5
25 65.5
26 65.5
27 65.5
28 65.5
29 34.5
30 7.3
31 29.1
32 25.5
33 29.1
34 36.4
35 52.7
36 69.1
37 69.1
38 69.1
39 69.1
40 69.1
41 69.1
42 69.1
43 69.1
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