View source: R/VDJ_contigs_to_vgm.R
VDJ_contigs_to_vgm | R Documentation |
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)
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. |
data frame with column names that match the VDJ_GEX_matrix output. Can be appended to the VDJ_GEX_matrix output
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")
})
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