segments.alphabets: Alphabets of TCR and Ig gene segments.

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

Character vector with names for segments. With tcR we provided alphabets for all alpha, beta, gamma and delta chains gene segments.

Usage

HUMAN_TRAV

HUMAN_TRAJ

HUMAN_TRBV

HUMAN_TRBD

HUMAN_TRBJ

HUMAN_TRBV_MITCR

HUMAN_TRBV_ALS

HUMAN_TRGV

HUMAN_TRGJ

HUMAN_TRDV

HUMAN_TRDD

HUMAN_TRDJ

MOUSE_TRBV

MOUSE_TRBJ

MOUSE_TRAV

MOUSE_TRAJ

MOUSE_IGKV

MOUSE_IGKJ

MOUSE_IGHV

MOUSE_IGHD

MOUSE_IGHJ

MACMUL_TRBV

MACMUL_TRBJ

HUMAN_IGHV

HUMAN_IGHD

HUMAN_IGHJ

HUMAN_IGLV

HUMAN_IGLJ

MOUSE_IGLJ

MOUSE_IGLV

Format

Each <SPECIES>_<GENES> is a character vector. <SPECIES> is an identifier of species, <GENES> is concatenated three identifiers of cell type ("TR**" for TCR, "IG**" for Ig), chain (e.g., "**A*" for alpha chains) and gene segment ("***V" for V(ariable) gene segment, "***J" for J(oining) gene segment, "***D" for D(iversity) gene segment).

Examples

## Not run: 
HUMAN_TRBV[1]  #  => "TRBV10-1"

## End(Not run)

Example output

Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: gridExtra

Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Loading required package: reshape2
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.

Attaching package: 'tcR'

The following object is masked from 'package:igraph':

    diversity

[1] "TRBV10-1"

tcR documentation built on July 2, 2020, 3:18 a.m.