clonRem {IMGTStatClonotype}R Documentation

CDR3-IMGT outlier length

Description

This function removes IMGT clonoypes (AA) with CDR3-IMGT outlier lengths depending on the studied species (for Homo sapiens by default >=45 and <=4).

Usage

clonRem(set, min = 4, max = 45)

Arguments

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

Value

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

Examples


data(MID1)
data(MID2)
MID1<-clonRem(MID1)
MID2<-clonRem(MID2)


[Package IMGTStatClonotype version 1.0.3 Index]