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

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

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

if (FALSE) {
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")
}