orleans: Sequencing data sample from NGS project.

In thierrycnam/igfuns: Analyzes of Ig sequencing data

Description

A dataset containing the molecular characterization information of antibody sequences

Usage

orleans

Format

A data frame with 421194 rows and 66 variables:

cdr3

CDR3 sequence, in AA

cdr3_seq

CDR3 sequence, in nt

chain_type

type of the chain, either heavy or light

clstr_id

id of cd-hit group

color

color code for clonal family

compartment

compartment: PBMC/MUCOSA

dbtype

database type: nt or aa

depth

depth of a read based on cd-hit

dh

D-gene information, with subfamily

dh2

D-gene information, 2 digits precision (allele information)

div_germ

divergence from germline in percentage

fraction

cdr3 similarity threshold

fraction.1

cd-hit similarity score

FREQ_R_CDR1

frequence Replacement in CDR1

FREQ_R_CDR2

frequence Replacement in CDR2

FREQ_R_FR1

frequence Replacement in FR1

FREQ_R_FR2

frequence Replacement in FR2

FREQ_R_FR3

frequence Replacement in FR3

FREQ_R_VREG

frequence Replacement in VREG

FREQ_S_CDR1

frequence Silent in CDR1

FREQ_S_CDR2

frequence Silent in CDR2

FREQ_S_FR1

frequence Silent in FR1

FREQ_S_FR2

frequence Silent in FR2

FREQ_S_FR3

frequence Silent in FR3

FREQ_S_VREG

frequence Silent in VREG

gravy_cdr3

hydrophobicity in CDR3

id2

clonotype family id

jh

J-gene information, with subfamily

jh2

J-gene information, 2 digits precision (allele information)

label_subtype

isotype label, IgA, IgG, IgM

length

CDR3 length, in nt

mutations

number of mutations in the V-region

name

sequence name

ncl_mut_cdr1

number of nt mutations in the cdr1

ncl_mut_cdr2

number of nt mutations in the cdr2

ncl_mut_fr1

number of nt mutations in the fr1

ncl_mut_fr2

number of nt mutations in the fr2

ncl_mut_fr3

number of nt mutations in the fr3

neg_ch_cdr3

negative charges in CDR3

pos_ch_cdr3

positive charges in CDR3

R_CDR1

Ratio R_CDR1

R_CDR2

Ratio R_CDR2

R_FR1

R_FR1

R_FR2

R_FR2

R_FR3

R_FR3

R_VREG

R_VREG

RS_CDR1

Ratio RS_CDR1

RS_CDR2

Ratio RS_CDR2

RS_FR1

RS_FR1

RS_FR2

RS_FR2

RS_FR3

RS_FR3

RS_VREG

RS_VREG

run

run id

S_CDR1

Ratio S_CDR1

S_CDR2

Ratio S_CDR2

S_FR1

S_FR1

S_FR2

S_FR2

S_FR3

S_FR3

S_VREG

S_VREG

sample

the sample

status

status of the patient, early-treated (PHI) or late-treated (CHI)

subtype

isotype found by BLAST

V

V-gene segment family

vh

V-gene information, with subfamily

vh2

V-gene information, 2 digits precision (allele information)

X

index created by R

Source

http://www.diamondse.info/

thierrycnam/igfuns documentation built on May 4, 2020, 3:21 a.m.