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"
loadContigs(input, format = "10X")A directory path containing contig files or a list/data frame of pre-loaded contig data.
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.
A list of contigs formatted for use with combineTCR() or
combineBCR(). Rows containing only NA values (aside from the barcode)
are dropped.
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")