contigs: SplitDataFrameList containing AIRR-seq (TCR) data for six...

In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

SplitDataFrameList containing AIRR-seq (TCR) data for six cells

Description

Data are a small subset of the TCR-seq data from the paper, "Progressive immune dysfunction with advancing disease stage in renal cell carcinoma" (Braun et al. 2021). The full dataset can be obtained from dbGap phs002252.v1.p1.

Usage

data(contigs)

Format

A SplitDataFrameList with six elements. Each list element contains the TCR-seq data for a single cell in a DFrame. Each DFrame has 19 variables and as many rows as there are contigs for the cell.

The variables in the dataset are the same as those in the contig_annotations.csv file created by 10X. The meaning of each variable label is specified at https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/output/annotation, but they are also summarized below:

barcode

Cell barcode for the contig in the list element.

is_cell

True or False value indicating whether the barcode was called as a cell.

contig_id

Unique identifier for this contig.

high_confidence

True or False value indicating whether the contig was called as high-confidence (unlikely to be a chimeric sequence or some other artifact).

length

The contig sequence length in nucleotides.

chain

The chain associated with this contig; for example, TRA, TRB, IGK, IGL, or IGH. A value of "Multi" indicates that segments from multiple chains were present.

v_gene

The highest-scoring V segment, for example, TRAV1-1.

d_gene

The highest-scoring D segment, for example, TRBD1.

j_gene

The highest-scoring J segment, for example, TRAJ1-1.

c_gene

The highest-scoring C segment, for example, TRAC.

full_length

If the contig was declared as full-length.

productive

If the contig was declared as productive.

cdr3

The predicted CDR3 amino acid sequence.

cdr3_nt

The predicted CDR3 nucleotide sequence.

reads

The number of reads aligned to this contig.

umis

The number of distinct UMIs aligned to this contig.

raw_clonotype_id

The ID of the clonotype to which this cell barcode was assigned.

raw_consensus_id

The ID of the consensus sequence to which this contig was assigned.

sample

Sample identifier. The data for contigs come from two different samples.

Source

Braun, David A., et al. "Progressive immune dysfunction with advancing disease stage in renal cell carcinoma." Cancer cell 39, no. 5 (2021): 632-648.

Examples

data('contigs')
x <- clonoStats(contigs)

kstreet13/VDJdive documentation built on May 27, 2023, 8:08 a.m.