TrustVDJ: Tools for Immune Repertoire Analysis

Read10x

R Documentation

Read AIRR/10x Report Files

Description

Read AIRR file and/or contig/consensus/clonotype file generated by 10x cellranger (> 6.0). Generally AIRR file: airr_rearrangement.tsv (from cellranger); contig files: all_contig_annotations.csv, filtered_contig_annotations.csv; consensus file: consensus_annotations.csv; clonotype file: clonotypes.csv. (.gz supported)

AIRR + filtered_contig: Read10x will read AIRR and add it 'consensus_id, fwr.., cdr.. and full_length' column based on filtered_contig file.
only one file: Read10x will return a data.frame for this file.
AIRR/contig + consensus/clonotype: Read10x will ignore consensus/clonotype file when either AIRR or contig file is given. Note that when AIRR + all_contig, only contigs in AIRR will be return.
consensus + clonotype (no AIRR nor contig): Read10x will add clonotype frequency to consensus file. (Don't worry about the information of inkt/mait_evidence in clonotype, these can be reproduced in downstream analysis.)

Usage

Read10x(
  airr_file = NULL,
  contig_file = NULL,
  consensus_file = NULL,
  clonotype_file = NULL,
  verbose = TRUE
)

Arguments

`airr_file`	character. Path to AIRR file.
`contig_file`	character. Path to contig_annotations file generated by 10x cellranger.
`consensus_file`	character. Path to consensus_annotations file generated by 10x cellranger.
`clonotype_file`	character. Path to clonotypes file generated by 10x cellranger.
`verbose`	logical. Print progress. Default is TRUE.

Value

A VDJ information data.frame

Examples

# file paths
airr_file      = system.file('extdata', '10x_airr_rearrangement.tsv.gz', package = 'TrustVDJ')
contig_file    = system.file('extdata', '10x_all_contig_annotations.csv.gz', package = 'TrustVDJ')
#or contig_file =
#system.file('extdata', '10x_filtered_contig_annotations.csv.gz', package = 'TrustVDJ')
consensus_file = system.file('extdata', '10x_consensus_annotations.csv.gz', package = 'TrustVDJ')
clonotype_file = system.file('extdata', '10x_clonotypes.csv.gz', package = 'TrustVDJ')

# both AIRR and contig

data = Read10x(airr_file = airr_file, contig_file = contig_file)
head(data)


# both consensus and clonotype
data = Read10x(consensus_file = consensus_file, clonotype_file = clonotype_file)
head(data)

# only AIRR
data = Read10x(airr_file = airr_file)
head(data)

# only contig
data = Read10x(contig_file = contig_file)
head(data)

# only consensus
data = Read10x(consensus_file = consensus_file)
head(data)

# only clonotype
data = Read10x(clonotype_file = clonotype_file)
head(data)

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.