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]