loadContigs: Loading the contigs derived from single-cell sequencing

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Loading the contigs derived from single-cell sequencing

Description

This function generates a contig list and formats the data to allow for function with combineTCR() or combineBCR(). If using data derived from filtered outputs of 10X Genomics, there is no need to use this function as the data is already compatible.

The files that this function parses includes:

• 10X: "filtered_contig_annotations.csv"

• AIRR: "airr_rearrangement.tsv"

• BD: "Contigs_AIRR.tsv"

• Dandelion: "all_contig_dandelion.tsv"

• Immcantation: "data.tsv"

• JSON: ".json"

• ParseBio: "barcode_report.tsv"

• MiXCR: "clones.tsv"

• Omniscope: ".csv"

• TRUST4: "barcode_report.tsv"

• WAT3R: "barcode_results.csv"

Usage

loadContigs(input, format = "10X")

Arguments

input	The directory in which contigs are located or a list with contig elements
format	The format of the single-cell contig, currently supporting: "10X", "AIRR", "BD", "Dandelion", "JSON", "MiXCR", "ParseBio", "Omniscope", "TRUST4", "WAT3R", and "Immcantation"

Value

List of contigs for compatibility with combineTCR() or combineBCR(). Note that rows which are fully NA are dropped from the final output.

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")

ncborcherding/scRepertoire documentation built on Feb. 14, 2025, 10:43 a.m.