ScCounts object — ScCounts-class • mcATAC

ScCounts is a data structure that contains the counts of reads for a set of cells in a set of genomic bins.

Slots

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)"
genome: genome assembly of the peaks. e.g. "hg38", "hg19", "mm9", "mm10"
data: a named list with sparse matrices for each chromosome. Each sparse matrix at position i,j contains the number of reads that map to the cell j in the genomic coordinate i (in 1 based format).
path: original path from which the object was loaded (optional)
genomic_bins: an intervals set with the genomic bins. Should have columns named "chrom", "start", "end" and "name" with the chromosome, start and end positions and name of the bin. The names of the data matrices are the "name" field. Note that even though the data is stored in 1-based format, the genomic bins are in 0-based format (misha format), hence the filenames are in 0-based format.