AIRR to Platypus V3 VGM compatibility function

Source: R/PlatypusDB_AIRR_to_VGM.R

Loads in and converts input AIRR-compatible tsv file(s) into the Platypus VGM object format.All compulsory AIRR data columns are needed. Additionally, the following columns are required: v_call, cell_id, clone_id. If trim.and.align is set to TRUE additionally the following columns are needed: v_sequence_start, j_sequence_end. Note on TRUST4 input: TRUST4 (https://doi.org/10.1038/s41592-021-01142-n2) is a newly alignment tool for VDJ data by the Shirley lab. It is able to also extract VDJ sequences from 10x GEX data. We are actively testing TRUST4 as an alternative to Cellranger and can not give recommendations as of now. This function does support the conversion of TRUST4 airr output data into the Platypus VGM format. In that case, an extra column will be added describing whether the full length VDJ sequence was extracted for any given cell and chain.

PlatypusDB_AIRR_to_VGM(
  AIRR.input,
  get.VDJ.stats,
  VDJ.combine,
  trim.and.align,
  filter.overlapping.barcodes.VDJ,
  group.id,
  verbose
)

Arguments

AIRR.input

Source of the AIRR table(s) as a list. There are 2 available input options: 1. 1. List with local paths to .tsv files / 3. List of AIRR tables loaded in as R objects within the current R environment.

get.VDJ.stats

Boolean. Defaults to TRUE. Whether to generate summary statistics on repertoires and output those as output_VGM[[3]]

VDJ.combine

Boolean. Defaults to TRUE. Whether to integrate repertoires. A sample identifier will be appended to each barcode both. Highy recommended for all later functions

trim.and.align

Boolean. defaults to FALSE. Whether to trim VJ/VDJ seqs and add information from alignment in AIRR dataframe columns. ! No alignment is done here, instead, columns containing alignment information in the AIRR dataframes are reformatted.

filter.overlapping.barcodes.VDJ

Boolean. defaults to TRUE. Whether to remove barcodes which are shared among samples in the GEX analysis. Shared barcodes normally appear at a very low rate.

group.id

vector with integers specifying the group membership. c(1,1,2,2) would specify the first two elements of the input AIRR list are in group 1 and the third/fourth input elements will be in group 2.

verbose

Writes runtime status to console. Defaults to FALSE

Value

A VDJ_GEX_Matrix object used in Platypus V3 as an input to most analysis and plotting functions

Examples

if (FALSE) {

VGM <- PlatypusDB_AIRR_to_VGM(AIRR.input =
list("~/pathto/s1/airr_rearrangement.tsv", "~pathto/s2/airr_rearrangement.tsv"),
VDJ.combine = TRUE, group.id = c(1,2), filter.overlapping.barcodes.VDJ = TRUE)
}