repGermline: Creates germlines for clonal lineages

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Creates germlines for clonal lineages

Description

This function creates germlines for clonal lineages. B cell clonal lineage represents a set of B cells that presumably have a common origin (arising from the same VDJ rearrangement event) and a common ancestor. Each clonal lineage has its own germline sequence that represents the ancestral sequence for each BCR in clonal lineage. In other words, germline sequence is a sequence of B-cells immediately after VDJ recombination, before B-cell maturation and hypermutation process. Germline sequence is useful for assessing the degree of mutation and maturity of the repertoire.

Usage

repGermline(.data, .species, .min_nuc_outside_cdr3, .threads)

Arguments

.data	The data to be processed. Can be data.frame, data.table or a list of these objects. It must have columns in the immunarch compatible format immunarch_data_format.
.species	Species from which the data was acquired. Available options: "HomoSapiens" (default), "MusMusculus", "BosTaurus", "CamelusDromedarius", "CanisLupusFamiliaris", "DanioRerio", "MacacaMulatta", "MusMusculusDomesticus", "MusMusculusCastaneus", "MusMusculusMolossinus", "MusMusculusMusculus", "MusSpretus", "OncorhynchusMykiss", "OrnithorhynchusAnatinus", "OryctolagusCuniculus", "RattusNorvegicus", "SusScrofa".
.min_nuc_outside_cdr3	This parameter sets how many nucleotides should have V or J chain outside of CDR3 to be considered good for further alignment.
.threads	Number of threads to use.

Value

Data with added columns: * Sequence (FR1+CDR1+FR2+CDR2+FR3+CDR3+FR4 in nucleotides; the column will be replaced if exists) * V.allele, J.allele (chosen alleles of V and J genes), * V.aa, J.aa (V and J sequences from original clonotype, outside CDR3, converted to amino acids) * Germline.sequence (combined germline nucleotide sequence)

Examples

data(bcrdata)

bcrdata$data %>%
  top(5) %>%
  repGermline()

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.