MID2 {IMGTStatClonotype}R Documentation

CD4+ population at Pre-vaccination IMGT/HighV-QUEST output

Description

The data of one set from IMGT/HighV-QUEST output used here as an example.

Usage

data("MID2")

Format

A data frame with 1882 observations on the following 26 variables:

cdr3aa: CDR3-IMGT sequence (AA)

expid: Experimental ID

clonoIndex: Representative sequence index

onecopy: Nb of '1 copy'

morethanone: Nb of 'More than one'

total: Total nb of '1 copy' and 'More than one'

indexes: '1 copy' Indexes

vgene: V-gene

vallele: V-allele

dgene: D-gene

dallele: D-allele

jgene: J-gene

jallele: J-allele

cdr1: CDR1-IMGT

cdr2: CDR2-IMGT

gcdr1: CDR1-IMGT gapped sequence (AA)

gcdr2: CDR2-IMGT gapped sequence (AA)

pid: % identity with the closest germline IMGT V gene and allele

length: Sequence length

c104: C104 (1st-CYS)

f118: F118 or W118 (J-PHE or J-TRP)

anchors: Anchors (C104, F118 or W118)

seqid: Sequence ID

functionality: Functionality

sequenceFileNumber: Sequence file number

sequenceClonoFileNumber: Sequence clonotype file number

Source

Sequencing data used for this example is available in the NCBI Sequence Read Archive under the accession code SRX326382. The description of this data is available in Li S. et al. (2013)

References

Alamyar E., Giudicelli V., Li S., Duroux P., Lefranc M-P. (2012) IMGT/High V-QUEST: The IMGT web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Research. 8:1:2. doi: 10.4172/1745-7580.1000056. PMID: 22647994.

Alamyar E., Duroux P., Lefranc M.-P. and Giudicelli V. (2012) IMGT tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT HighV-QUEST for NGS. Methods Mol. Biol. 882:569-604. doi: 10.1007/978-1-61779-842-9_32. PMID: 22665256.

Li S., Lefranc M.-P., Miles J.J., Alamyar E., Giudicelli V., Duroux P., et al. (2013) IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nature Communications. 4:2333. doi: 10.1038/ncomms3333. PMID: 23995877.

Examples


 data(MID2)
 str(MID2)


[Package IMGTStatClonotype version 1.0.3 Index]