VDJ_contigs_to_vgm: Formats "VDJ_contigs_annotations.csv" files from cell ranger...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Formats "VDJ_contigs_annotations.csv" files from cell ranger to match the VDJ_GEX_matrix output using only cells with 1VDJ and 1VJ chain

Description

Formats "VDJ_contigs_annotations.csv" files from cell ranger to match the VDJ_GEX_matrix output using only cells with 1VDJ and 1VJ chain

Usage

VDJ_contigs_to_vgm(directory, sample.names, celltype, FB, platypus.version)

Arguments

directory	list containing paths to the "filtered_contig_annotations.csv" files from cell ranger.
sample.names	vector specifying sample names.
celltype	Character. Either "Tcells" or "Bcells".
FB	Integer specifying whether VGM should contain Feature Barcode columns or not. Default set to FALSE.
platypus.version	Function based on VGM object from V3, no need to set this parameter.

Value

data frame with column names that match the VDJ_GEX_matrix output. Can be appended to the VDJ_GEX_matrix output

Examples

try({
directory.list <- list()
directory.list[[1]] <- c("~/Dataset_1/filtered_contig_annotations.csv")
directory.list[[2]] <- c("~/Dataset_1/filtered_contig_annotations.csv")
filtered_contig_vgm <- VDJ_contigs_to_vgm(directory = directory.list,
sample.names = c(s3,s4), celltype = "Tcells")
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.