searchPublished: Search for T cell receptor beta CDR3 amino acid sequences...

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

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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. 1, 2018, 3:54 a.m.