The function reads the "outs/atac_fragments.tsv.gz" file, and "outs/filtered_feature_bc_matrix/barcodes.tsv.gz" file and writes an ScCounts object to "out_dir".
Usage
scc_from_10x(
input_dir,
out_dir,
cell_suffix = NULL,
genome = NULL,
bin_size = 50000000,
overwrite = FALSE,
id = "",
description = "",
verbose = FALSE,
tabix_bin = "tabix",
chromosomes = NULL
)
write_sc_counts_from_10x(
input_dir,
out_dir,
cell_suffix = NULL,
genome = NULL,
bin_size = 50000000,
overwrite = FALSE,
id = "",
description = "",
verbose = FALSE,
tabix_bin = "tabix",
chromosomes = NULL
)Arguments
- input_dir
path to the 10x 'outs' directory
- out_dir
output directory.
- cell_suffix
a suffix to add to the cell names (optional). This is useful when you want to merge multiple batches of cells. The suffix would be added in the following way:
paste0(cell_name, "-", cell_suffix).- bin_size
Size of the genomic bins to use (in bp). Each chromsome will be chunked into bins with size which is smaller than this value. Default is 50Mb.
- overwrite
overwrite existing directory (optional)
- id
an identifier for the object, e.g. "pbmc".
- description
description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)"
- verbose
verbose output (optional)
- tabix_bin
path to the tabix binary (optional)
- chromosomes
process only specific chromosomes (optional).