MID2 {IMGTStatClonotype} | R Documentation |
The data of one set from IMGT/HighV-QUEST output used here as an example.
data("MID2")
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
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)
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.
data(MID2) str(MID2)