read_cellranger_outs2: Read and preprocess the contig_annotation file from 10X...

In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

Read and preprocess the contig_annotation file from 10X Genomics' cellranger output and return a concatenated data frame

Description

This function has been reduced from read_cellranger_outs. Most important change is that CDR3 sequences from equal clonotype_ids are not shared across the clonotype. In principle this function will only read the filtered_contig_annotations.csv and filtered_contig.fasta and joins them.

Usage

read_cellranger_outs2(vdj_outs_path)

Arguments

vdj_outs_path

named vector of paths to the outs-folder (or any folders containing the necessary file, specified above); names will be added as "sample"-column to the output data frame

Value

data frame (cl_long)

Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.