VDJ_to_AIRR: Function to convert VDJ dataframe into an AIRR-formatted TSV...

In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

Function to convert VDJ dataframe into an AIRR-formatted TSV file.

Description

Takes a VDJ dataframe along with the imported IgBLAST annotations and alignments and converts it into a tab-separated values (TSV) file formatted according to the AIRR (Adaptive Immune Receptor Repertoire) guidelines.

Usage

VDJ_to_AIRR(
  VDJ,
  include,
  columns,
  complete.rows.only,
  filter.rows.with.stop.codons,
  output.file
)

Arguments

VDJ	dataframe - VDJ object as obtained from the 'VDJ_build()' function in Platypus, together with the imported IgBLAST annotations and alignments, as obtained from the 'import_IgBLAST_annotations' function in AntibodyForests.
include	list - a nested list specifying the samples and their associated clonotypes to include in the output TSV file. Each sublist represents a sample, where the sublist name is the sample name and the elements within the sublist are the clonotypes of that sample. If not provided, all samples and clonotypes are included.
columns	list - a list specifying the columns to include in the output TSV file. At minimum, the following columns must be specified: 'sequence_id', 'clone_id', 'sequence', 'sequence_alignment', 'germline_alignment', 'v_call', 'v_sequence_start', 'v_sequence_end', 'v_germline_start', 'v_germline_end', 'j_call', 'j_sequence_start', 'j_sequence_end', 'j_germline_start', and 'j_germline_end'. The items in this list should correspond to the column names in the VDJ dataframe, while the names of the items in this list should refer to the column names of the output TSV file.
complete.rows.only	bool - if TRUE, only complete rows (without any missing values) are included in the output TSV file. If FALSE, rows with missing values are retained in the output. Defaults to TRUE.
filter.rows.with.stop.codons	bool - if TRUE, rows containing sequences with stop codons (TAA, TAG, TGA) in the 'sequence_alignment' and 'germline_alignment' columns are filtered out from the output TSV file. Defaults to TRUE.
output.file	string - string specifying the path to the output file. If no path is specified, the output is written to 'airr_rearrengement.tsv' in the current working directory.

Value

None

Examples

## Not run: 
VDJ_to_AIRR(VDJ = VDJ_IgBLAST, output.file = "path/to/output.tsv")

## End(Not run)

AntibodyForests documentation built on April 4, 2025, 4:45 a.m.