aaseqtab: Summary of amino acid sequences of B cells of one individual

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

Data frame represents an output from IMGT/HighV-QUEST, file 5_AA-sequences(...).txt

Usage

data("aaseqtab")

Format

A data frame with 3000 observations on the following 18 variables.

Sequence_number

a numeric vector

Sequence_ID

a character vector

Functionality

a character vector

V_GENE_and_allele

a character vector

J_GENE_and_allele

a character vector

D_GENE_and_allele

a character vector

V_D_J_REGION

a character vector

V_J_REGION

a character vector

V_REGION

a character vector

FR1_IMGT

a character vector

CDR1_IMGT

a character vector

FR2_IMGT

a character vector

CDR2_IMGT

a character vector

FR3_IMGT

a character vector

CDR3_IMGT

a character vector

JUNCTION

a character vector

J_REGION

a character vector

FR4_IMGT

a character vector

References

Alamyar, E. et al., IMGT/HighV-QUEST: A High-Throughput System and Web Portal for the Analysis of Rearranged Nucleotide Sequences of Antigen Receptors, JOBIM 2010, Paper 63 (2010).

Brochet, X. et al., Nucl. Acids Res. 36, W503-508 (2008). PMID: 18503082

IMGT/HighV-QUEST 5_AA-sequences file description: http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#EAA

Examples

data(aaseqtab)
str(aaseqtab)

Example output

'data.frame':	3000 obs. of  18 variables:
 $ Sequence_number  : int  1 2 3 4 5 6 7 8 9 10 ...
 $ Sequence_ID      : chr  "Sequence1" "Sequence2" "Sequence3" "Sequence4" ...
 $ Functionality    : chr  "productive" "productive" "productive" "productive" ...
 $ V_GENE_and_allele: chr  "Homsap IGHV4-34*01 F, or Homsap IGHV4-34*02 F" "Homsap IGHV1-8*01 F" "Homsap IGHV1-3*01 F" "Homsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F" ...
 $ J_GENE_and_allele: chr  "Homsap IGHJ4*02 F" "Homsap IGHJ6*02 F" "Homsap IGHJ4*02 F" "Homsap IGHJ6*02 F" ...
 $ D_GENE_and_allele: chr  "Homsap IGHD6-25*01 F" "Homsap IGHD1-14*01 ORF" "Homsap IGHD6-19*01 F" "Homsap IGHD5-18*01 F" ...
 $ V_D_J_REGION     : chr  "SETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFFLKLSSVTAADTAVYYCARGCEESLIGVVQRCLDYWGQGTLVTVSS" "ASVKVSCKASGYTFTSYDINWVRQATGQGLEWMGWMNPNSGNTGYAQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCASHRVDPHFYYYYGMDVWGQGATVTVSS" "ASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCAREGSSGWYPNLDYWGQGTLVTVSS" "GESLKISCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGGLDTTMVDYYYGMDVWGQGTTVTVSS" ...
 $ V_J_REGION       : logi  NA NA NA NA NA NA ...
 $ V_REGION         : chr  "SETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFFLKLSSVTAADTAVYYCAR" "ASVKVSCKASGYTFTSYDINWVRQATGQGLEWMGWMNPNSGNTGYAQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCA" "ASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYCAR" "GESLKISCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAK" ...
 $ FR1_IMGT         : chr  "SETLSLTCAVY" "ASVKVSCKAS" "ASVKVSCKAS" "GESLKISCAAS" ...
 $ CDR1_IMGT        : chr  "GGSFSGYY" "GYTFTSYD" "GYTFTSYA" "GFTFSSYA" ...
 $ FR2_IMGT         : chr  "WSWIRQPPGKGLEWIGE" "INWVRQATGQGLEWMGW" "MHWVRQAPGQRLEWMGW" "MSWVRQAPGKGLEWVSA" ...
 $ CDR2_IMGT        : chr  "INHSGST" "MNPNSGNT" "INAGNGNT" "ISGSGGST" ...
 $ FR3_IMGT         : chr  "NYNPSLKSRVTISVDTSKNQFFLKLSSVTAADTAVYYC" "GYAQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYC" "KYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYC" "YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYC" ...
 $ CDR3_IMGT        : chr  "ARGCEESLIGVVQRCLDY" "ASHRVDPHFYYYYGMDV" "AREGSSGWYPNLDY" "AKDGGLDTTMVDYYYGMDV" ...
 $ JUNCTION         : chr  "CARGCEESLIGVVQRCLDYW" "CASHRVDPHFYYYYGMDVW" "CAREGSSGWYPNLDYW" "CAKDGGLDTTMVDYYYGMDVW" ...
 $ J_REGION         : chr  "DYWGQGTLVTVSS" "YYYYGMDVWGQGATVTVSS" "LDYWGQGTLVTVSS" "YYYGMDVWGQGTTVTVSS" ...
 $ FR4_IMGT         : chr  "WGQGTLVTVSS" "WGQGATVTVSS" "WGQGTLVTVSS" "WGQGTTVTVSS" ...

bcRep documentation built on May 2, 2019, 5:14 a.m.