clonRem {IMGTStatClonotype} | R Documentation |
This function removes IMGT clonoypes (AA) with CDR3-IMGT outlier lengths depending on the studied species (for Homo sapiens by default >=45 and <=4).
clonRem(set, min = 4, max = 45)
set |
the set from the IMGT/HighV-QUEST output to be compared |
min |
the lower level of CDR3-IMGT length |
max |
the upper level of CDR3-IMGT length |
This function returns sets from the IMGT/HighV-QUEST output without IMGT clonotypes (AA) having CDR3-IMGT outlier lengths. A matrix of 25 columns:
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 |
data(MID1) data(MID2) MID1<-clonRem(MID1) MID2<-clonRem(MID2)