Count snATAC-seq data matrix with Paired Insertion Counting (PIC)
PIC_counting.RdCount snATAC-seq data matrix with Paired Insertion Counting (PIC)
Usage
PIC_counting(
cells,
fragment_tsv_gz_file_location,
peak_sets,
deduplicate = FALSE,
load_full = TRUE,
extend_size = 5L,
verbose = TRUE
)Arguments
- cells
The cell barcode lables as a Character vector
- fragment_tsv_gz_file_location
The 10X Cell Ranger output fragment.tsv.gz file location. This can usually be found at the /out directory from Cell Ranger output
- peak_sets
The set of peaks as a GenomicRanges object. This will be the features for the data matrix. Alternatively, this can be a data.frame and the function will convert it into a GenomicRanges object
- deduplicate
Whether to include deduplicate step where within the same cell, fragments with identical start and end location will be deduplicated. This is usually unnecessisary from Cell Ranger ATAC output, since Cell Ranger ATAC has already deduplicated the fragments. But for dsc-ATAC-seq data, this step will be helpful and recommended.
- load_full
Whether to load the whole fragment.tsv.gz file into memory. If set to FALSE, the function will load it dynamically to save RAM
- extend_size
How long should we extend the exact insertion site as accessible window
- verbose
Whether to output progress information including the progress bar