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Load Immune Receptor Sequencing Contigs

Source: R/loadContigs.R
loadContigs.Rd

This function loads and processes contig data from various single-cell immune receptor sequencing formats. It reads data from a directory (recursively) or from an already loaded list/data frame, transforms it to a common structure, and returns a list of contigs ready for downstream analysis with combineTCR() or combineBCR().

Supported file formats and their expected file names:

  • 10X: "filtered_contig_annotations.csv"

  • AIRR: "airr_rearrangement.tsv"

  • BD: "Contigs_AIRR.tsv"

  • Dandelion: "all_contig_dandelion.tsv"

  • Immcantation: "_data.tsv" (or similar)

  • “JSON`: ".json"

  • ParseBio: "barcode_report.tsv"

  • MiXCR: "clones.tsv"

  • TRUST4: "barcode_report.tsv"

  • WAT3R: "barcode_results.csv"

Usage

loadContigs(input, format = "10X")

Arguments

input

A directory path containing contig files or a list/data frame of pre-loaded contig data.

format

A string specifying the data format. Must be one of: auto, 10X, AIRR, BD, Dandelion, JSON, MiXCR, ParseBio, TRUST4, WAT3R, or Immcantation. If "auto", the function attempts automatic format detection.

Value

A list of contigs formatted for use with combineTCR() or combineBCR(). Rows containing only NA values (aside from the barcode) are dropped.

Examples

TRUST4 <- read.csv("https://www.borch.dev/uploads/contigs/TRUST4_contigs.csv")
contig.list <- loadContigs(TRUST4, format = "TRUST4")

BD <- read.csv("https://www.borch.dev/uploads/contigs/BD_contigs.csv")
contig.list <- loadContigs(BD, format = "BD")

WAT3R <- read.csv("https://www.borch.dev/uploads/contigs/WAT3R_contigs.csv")
contig.list <- loadContigs(WAT3R, format = "WAT3R")