README.md

In victoraLab/clonality: Easily Define Groups Of T/B Cells

clonality

The clonality package function helps to define B or T cell repertoire clonality automatically.

Instalation:

devtools::install_github("victoraLab/clonality")

How to use it:

The tra and trb objects are small sequencing datasets that can be used as a test

head(tra)
clonality(data =  tra, output =  "tra.output")

On B cells: Running the function on a xlsx file containing BCR sequences and getting clonal subclusters (mismatch parameter) that have up to 20% CDR3 differences based on the string aligment, (restricted Damerau-Levenshtein distance from stringdist package).

clonality(data = "example.xlsx",
ident_col = "Sequence_ID",
vgene_col = "V_GENE_and_allele",
jgene_col = "J_GENE_and_allele",
cdr3_col = "AA_JUNCTION",
cell = "B",
mismatch = 0.2)

On T cells: Running the function on a xlsx file containing TCR sequences and without subclustering, only identical sequences based on V gene, J gene, and CDR3 sequence will cluster.

clonality(data = "example.xlsx",
ident_col = "Sequence_ID",
vgene_col = "V_GENE_and_allele",
jgene_col = "J_GENE_and_allele",
cdr3_col = "AA_JUNCTION",
cell = "T",
mismatch = 0)

The function can also be used on a data.frame like:

clonality(data = my_tcr, output = "output")

This package also has a function to call and import clonality on the filtered_contig_annotations file from 10x genomics experiments.

Use the sticky parameter = TRUE to map cells with only one chain to cells with the paired sequence.

tenx(data = filtered_contig_annotations, method = "sticky_ends", cell = "T", only_productive = T)
seu <- add_seurat_metadata(seu = singlets,  clonal.list = ls(pattern = "^Clonal"), sticky = T, purity = 0.8)

victoraLab/clonality documentation built on March 19, 2024, 7:41 p.m.